Use bakrep-v2 api

* Update api url
* Make md5 and size from result file object optional

Author: lukasjelonek

bakrep/model.py

@@ -33,7 +33,7 @@ def matches(self, filters: List[dict]):
 
     @staticmethod
     def from_dict(dict: dict):
-        return Result(dict['url'], dict['attributes'], dict['md5'], dict['size'])
+        return Result(dict['url'], dict['attributes'], dict['md5'] if 'md5' in dict else "", dict['size'] if 'size' in dict else 0)
 
 
 class Dataset:
@@ -160,7 +160,7 @@ class DownloadFailedException(Exception):
 
 
 class BakrepDownloader:
-    def __init__(self, url: str = "https://bakrep.computational.bio/api/v1/datasets/"):
+    def __init__(self, url: str = "https://bakrep.computational.bio/api/v2/datasets/"):
         self.url = url
 
     def download(self, id: str, filters: List[dict], target_directory: str):

test/test_download.py

@@ -6,7 +6,7 @@
 
 
 def mockdataset(m, id):
-    m.get(f"https://bakrep.computational.bio/api/v1/datasets/{id}",
+    m.get(f"https://bakrep.computational.bio/api/v2/datasets/{id}",
           content=Path(f"./test/data/scenarios/download-dataset/{id}.json").read_bytes())
 
 
@@ -73,7 +73,7 @@ def test_download_dataset_fails_should_raise_exception(self):
         with requests_mock.Mocker() as m:
             id = "SAMEA3231284"
             m.get(
-                f"https://bakrep.computational.bio/api/v1/datasets/{id}", status_code=404)
+                f"https://bakrep.computational.bio/api/v2/datasets/{id}", status_code=404)
             with tempfile.TemporaryDirectory() as tmp:
                 d = BakrepDownloader()
                 self.assertRaises(DownloadFailedException, lambda: d.download(

test/test_download_command.py

@@ -7,13 +7,10 @@
 from bakrep.cli import main
 
 
-def mock_result(id: str, suffix: str, attributes: dict,
-                md5="d41d8cd98f00b204e9800998ecf8427e"  # md5 sum for no content
-                ):
+def mock_result(id: str, suffix: str, attributes: dict):
     return {
         "url": f"https://bakrep-data.s3.computational.bio.uni-giessen.de/{id}/{id}.{suffix}",
         "attributes": attributes,
-        "md5": md5,
         "size": 0,
     }
 
@@ -25,7 +22,7 @@ def mock_dataset(m: Mocker, id: str):
         mock_result(id, "json", {"tool": "test", "filetype": "json"})
     ]}
     m.get(
-        f"https://bakrep.computational.bio/api/v1/datasets/{id}", json=dataset)
+        f"https://bakrep.computational.bio/api/v2/datasets/{id}", json=dataset)
     for r in dataset["results"]:
         m.get(r['url'], text='')