From e46bffe80fa54cb53cc2b9106ed90f834165bc2b Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Fri, 19 Apr 2024 17:08:37 +0100
Subject: [PATCH] changes on cbioportal download system.

---
 pypgatk/cgenomes/cbioportal_downloader.py | 8 ++++----
 pypgatk/config/cbioportal_config.yaml     | 4 ++--
 2 files changed, 6 insertions(+), 6 deletions(-)

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: