pubkey added (#36)

Co-authored-by: Thomas Zajac <[email protected]>

ghga_connector/__init__.py

@@ -17,4 +17,4 @@
 CLI - Client to perform up- and download operations to and from a local ghga instance
 """
 
-__version__ = "0.2.1"
+__version__ = "0.2.2"

ghga_connector/cli.py

@@ -59,16 +59,23 @@ def upload(  # noqa C901
     *,
     file_id: str = typer.Option(..., help="The id if the file to upload"),
     file_path: Path = typer.Option(..., help="The path to the file to upload"),
+    pubkey_path: Path = typer.Argument(
+        "./key.pub",
+        help="The path to a public key from the key pair that was used to encrypt the "
+        + "crypt4gh envelope. Defaults to the file key.pub in the current folder.",
+    ),
 ):
     """
     Command to upload a file
     """
     core.RequestsSession.configure(config.max_retries)
+
     core.upload(
         api_url=config.upload_api,
         file_id=file_id,
         file_path=file_path,
         message_display=CLIMessageDisplay(),
+        pubkey_path=pubkey_path,
     )
 
 

ghga_connector/core/api_calls.py

@@ -18,11 +18,14 @@
 Contains calls to the GHGA storage API
 """
 
+import base64
 import json
 from enum import Enum
+from pathlib import Path
 from time import sleep
 from typing import Dict, Iterator, Tuple, Union
 
+import crypt4gh.keys
 import requests
 from requests.structures import CaseInsensitiveDict
 
@@ -51,7 +54,12 @@ class UploadStatus(str, Enum):
     UPLOADED = "uploaded"
 
 
-def initiate_multipart_upload(*, api_url: str, file_id: str) -> Tuple[str, int]:
+def initiate_multipart_upload(
+    *,
+    api_url: str,
+    file_id: str,
+    pubkey_path: Path,
+) -> Tuple[str, int]:
     """
     Perform a RESTful API call to initiate a multipart upload
     Returns an upload id and a part size
@@ -60,7 +68,9 @@ def initiate_multipart_upload(*, api_url: str, file_id: str) -> Tuple[str, int]:
     # build url and headers
     url = f"{api_url}/uploads"
     headers = {"Accept": "application/json", "Content-Type": "application/json"}
-    post_data = {"file_id": file_id}
+    public_key = base64.b64encode(crypt4gh.keys.get_public_key(pubkey_path)).decode()
+
+    post_data = {"file_id": file_id, "public_key": public_key}
     serialized_data = json.dumps(post_data)
 
     # Make function call to get upload url
@@ -344,12 +354,18 @@ def download_api_call(
     return download_url, file_size, NO_RETRY_TIME
 
 
-def start_multipart_upload(*, api_url: str, file_id: str) -> Tuple[str, int]:
+def start_multipart_upload(
+    *, api_url: str, file_id: str, pubkey_path: Path
+) -> Tuple[str, int]:
     """Try to initiate a multipart upload. If it fails, try to cancel the current upload
     can and then try to initiate a multipart upload again."""
 
     try:
-        multipart_upload = initiate_multipart_upload(api_url=api_url, file_id=file_id)
+        multipart_upload = initiate_multipart_upload(
+            api_url=api_url,
+            file_id=file_id,
+            pubkey_path=pubkey_path,
+        )
         return multipart_upload
     except exceptions.NoUploadPossibleError as error:
         file_metadata = get_file_metadata(api_url=api_url, file_id=file_id)
@@ -363,7 +379,9 @@ def start_multipart_upload(*, api_url: str, file_id: str) -> Tuple[str, int]:
             upload_status=UploadStatus.CANCELLED,
         )
 
-        multipart_upload = initiate_multipart_upload(api_url=api_url, file_id=file_id)
+        multipart_upload = initiate_multipart_upload(
+            api_url=api_url, file_id=file_id, pubkey_path=pubkey_path
+        )
 
     except Exception as error:
         raise error

ghga_connector/core/exceptions.py

@@ -41,13 +41,21 @@ def __init__(self, *, output_file: str):
 
 
 class FileDoesNotExistError(RuntimeError):
-    """Thrown, when the specified file already exists."""
+    """Thrown, when the specified file does not exist."""
 
     def __init__(self, *, file_path: Path):
         message = f"The file {file_path} does not exist."
         super().__init__(message)
 
 
+class PubKeyFileDoesNotExistError(RuntimeError):
+    """Thrown, when the specified public key file already exists."""
+
+    def __init__(self, *, pubkey_path: Path):
+        message = f"The public key file {pubkey_path} does not exist."
+        super().__init__(message)
+
+
 class ApiNotReachableError(RuntimeError):
     """Thrown, when the api is not reachable."""
 

ghga_connector/core/main.py

@@ -50,17 +50,22 @@ def check_url(api_url, *, wait_time=1000) -> bool:
     return True
 
 
-def upload(  # noqa C901, pylint: disable=too-many-statements
+def upload(  # noqa C901, pylint: disable=too-many-statements,too-many-branches
     *,
     api_url: str,
     file_id: str,
     file_path: Path,
     message_display: AbstractMessageDisplay,
+    pubkey_path: Path,
 ) -> None:
     """
     Core command to upload a file. Can be called by CLI, GUI, etc.
     """
 
+    if not os.path.isfile(pubkey_path):
+        message_display.failure(f"The file {pubkey_path} does not exist.")
+        raise exceptions.PubKeyFileDoesNotExistError(pubkey_path=pubkey_path)
+
     if not os.path.isfile(file_path):
         message_display.failure(f"The file {file_path} does not exist.")
         raise exceptions.FileDoesNotExistError(file_path=file_path)
@@ -70,7 +75,9 @@ def upload(  # noqa C901, pylint: disable=too-many-statements
         raise exceptions.ApiNotReachableError(api_url=api_url)
 
     try:
-        upload_id, part_size = start_multipart_upload(api_url=api_url, file_id=file_id)
+        upload_id, part_size = start_multipart_upload(
+            api_url=api_url, file_id=file_id, pubkey_path=pubkey_path
+        )
     except exceptions.NoUploadPossibleError as error:
         message_display.failure(
             f"This user can't start a multipart upload for the file_id '{file_id}'"

scripts/license_checker.py

@@ -69,7 +69,7 @@
 ]
 
 # exclude file by file ending from license header check:
-EXCLUDE_ENDINGS = ["json", "pyc", "yaml", "yml", "md", "html", "xml"]
+EXCLUDE_ENDINGS = ["json", "pub", "pyc", "sec", "yaml", "yml", "md", "html", "xml"]
 
 # exclude any files with names that match any of the following regex:
 EXCLUDE_PATTERN = [r".*\.egg-info.*", r".*__cache__.*", r".*\.git.*"]

setup.cfg

@@ -35,9 +35,10 @@ zip_safe = False
 include_package_data = True
 packages = find:
 install_requires =
-    ghga-service-chassis-lib[s3]==0.15.1
-    httpyexpect==0.2.2
+    ghga-service-chassis-lib[s3]==0.16.1
+    httpyexpect==0.2.4
     typer==0.4.1
+    crypt4gh==1.6
 
 python_requires = >= 3.9.10
 
@@ -47,7 +48,7 @@ console_scripts =
 
 [options.extras_require]
 dev =
-    ghga-service-chassis-lib[dev]==0.15.1
+    ghga-service-chassis-lib[dev]==0.16.1
     fastapi
     uvicorn
 

tests/fixtures/keypair/key.pub

@@ -0,0 +1,3 @@
+-----BEGIN CRYPT4GH PUBLIC KEY-----
+P1oBHfr9AA37Kg8WW79RKKpDZlp77KoFx+n+3sLzPBY=
+-----END CRYPT4GH PUBLIC KEY-----

tests/fixtures/keypair/key.sec

@@ -0,0 +1,3 @@
+-----BEGIN CRYPT4GH PRIVATE KEY-----
+YzRnaC12MQAEbm9uZQAEbm9uZQAgvT/vZ90UMmestkwn/7GDRU4uCxzz91KvP017CjYyY0Q=
+-----END CRYPT4GH PRIVATE KEY-----

tests/integration/test_cli.py

@@ -34,6 +34,9 @@
 from tests.fixtures.config import get_test_config
 from tests.fixtures.mock_api.testcontainer import MockAPIContainer
 from tests.fixtures.s3 import S3Fixture, get_big_s3_object, s3_fixture  # noqa: F401
+from tests.fixtures.utils import BASE_DIR
+
+PUBLIC_KEY_FILE = BASE_DIR / "keypair/key.pub"
 
 
 @pytest.mark.parametrize(
@@ -184,6 +187,7 @@ def test_upload(
                 upload(
                     file_id=uploadable_file.file_id,
                     file_path=uploadable_file.file_path.resolve(),
+                    pubkey_path=Path(PUBLIC_KEY_FILE),
                 )
 
                 s3_fixture.storage.complete_multipart_upload(
@@ -259,6 +263,7 @@ def test_multipart_upload(
                 upload(
                     file_id=file_id,
                     file_path=Path(file.name),
+                    pubkey_path=Path(PUBLIC_KEY_FILE),
                 )
 
         # confirm upload