diff --git a/pypgatk/cgenomes/cbioportal_downloader.py b/pypgatk/cgenomes/cbioportal_downloader.py index 60ae7fb..7e39810 100644 --- a/pypgatk/cgenomes/cbioportal_downloader.py +++ b/pypgatk/cgenomes/cbioportal_downloader.py @@ -34,8 +34,8 @@ def __init__(self, config_data, pipeline_arguments): self._list_studies = [] self._multithreading = True - self._cbioportal_base_url = 'https://www.cbioportal.org/webservice.do' - self._cancer_studies_command = 'cmd=getCancerStudies' + self._cbioportal_base_url = 'https://www.cbioportal.org/api' + self._cancer_studies_command = 'studies' self._cbioportal_download_url = 'https://cbioportal-datahub.s3.amazonaws.com' @@ -111,13 +111,13 @@ def get_cancer_studies(self): """ server = self._cbioportal_base_url endpoint = self._cancer_studies_command - self._cbioportal_studies = call_api_raw(server + "?" + endpoint).text + self._cbioportal_studies = call_api_raw(server + "/" + endpoint).text return self._cbioportal_studies def download_study(self, download_study, url_file_name=None): """ This function will download a study from cBioPortal using the study ID - :param download_study: Study to be download, if the study is empty or None, all the studies will be + :param download_study: Study to be downloaded, if the study is empty or None, all the studies will be downloaded. :param url_file_name: file tsv containing the urls to be downloaded. :return: None diff --git a/pypgatk/config/cbioportal_config.yaml b/pypgatk/config/cbioportal_config.yaml index 6be78e1..1aace6d 100644 --- a/pypgatk/config/cbioportal_config.yaml +++ b/pypgatk/config/cbioportal_config.yaml @@ -2,8 +2,8 @@ cbioportal_data_downloader: output_directory: database_cbioportal list_studies: [] cbioportal_api: - base_url: https://www.cbioportal.org/webservice.do - cancer_studies: cmd=getCancerStudies + base_url: https://www.cbioportal.org/api + cancer_studies: studies cbioportal_download_url: https://cbioportal-datahub.s3.amazonaws.com logger: formatters: