Merge branch 'master' into fix/delete_expired_refresh

fence/__init__.py

@@ -239,7 +239,7 @@ def _check_azure_storage(app):
             logger.debug(err)
 
 
-def _check_aws_creds_and_region(app):
+def _check_buckets_aws_creds_and_region(app):
     """
     Function to ensure that all s3_buckets have a valid credential.
     Additionally, if there is no region it will produce a warning
@@ -248,6 +248,7 @@ def _check_aws_creds_and_region(app):
     buckets = config.get("S3_BUCKETS") or {}
     aws_creds = config.get("AWS_CREDENTIALS") or {}
 
+    # check that AWS creds and regions are configured
     for bucket_name, bucket_details in buckets.items():
         cred = bucket_details.get("cred")
         region = bucket_details.get("region")
@@ -302,6 +303,16 @@ def _check_aws_creds_and_region(app):
             )
         )
 
+    # check that all the configured buckets are in `S3_BUCKETS`
+    bucket_names = config["ALLOWED_DATA_UPLOAD_BUCKETS"] or []
+    if config["DATA_UPLOAD_BUCKET"]:
+        bucket_names.append(config["DATA_UPLOAD_BUCKET"])
+    for bucket_name in bucket_names:
+        if bucket_name not in buckets:
+            logger.warning(
+                f"Data upload bucket '{bucket_name}' is not configured in 'S3_BUCKETS'"
+            )
+
 
 def app_config(
     app,
@@ -358,7 +369,7 @@ def app_config(
     _setup_oidc_clients(app)
 
     with app.app_context():
-        _check_aws_creds_and_region(app)
+        _check_buckets_aws_creds_and_region(app)
         _check_azure_storage(app)
 
 

fence/auth.py

@@ -1,5 +1,6 @@
 import flask
 from flask_sqlalchemy_session import current_session
+from datetime import datetime
 from functools import wraps
 import urllib.request, urllib.parse, urllib.error
 
@@ -98,6 +99,7 @@ def set_flask_session_values(user):
     if user:
         _update_users_email(user, email)
         _update_users_id_from_idp(user, id_from_idp)
+        _update_users_last_auth(user)
 
         #  This expression is relevant to those users who already have user and
         #  idp info persisted to the database. We return early to avoid
@@ -298,3 +300,14 @@ def _update_users_id_from_idp(user, id_from_idp):
 
         current_session.add(user)
         current_session.commit()
+
+
+def _update_users_last_auth(user):
+    """
+    Update _last_auth.
+    """
+    logger.info(f"Updating username {user.username}'s _last_auth.")
+    user._last_auth = datetime.now()
+
+    current_session.add(user)
+    current_session.commit()

fence/blueprints/data/blueprint.py

@@ -1,6 +1,7 @@
 import flask
 
 from cdislogging import get_logger
+from cdispyutils.config import get_value
 
 from fence.auth import login_required, require_auth_header, current_token, get_jwt
 from fence.authz.auth import check_arborist_auth
@@ -9,8 +10,7 @@
     IndexedFile,
     get_signed_url_for_file,
 )
-from fence.config import config
-from fence.errors import Forbidden, InternalError, UserError, Forbidden
+from fence.errors import Forbidden, InternalError, UserError, Unauthorized
 from fence.resources.audit.utils import enable_audit_logging
 from fence.utils import get_valid_expiration
 
@@ -175,11 +175,24 @@ def upload_data_file():
     )
 
     protocol = params["protocol"] if "protocol" in params else None
+    bucket = params.get("bucket")
+    if bucket:
+        s3_buckets = get_value(
+            flask.current_app.config,
+            "ALLOWED_DATA_UPLOAD_BUCKETS",
+            InternalError("ALLOWED_DATA_UPLOAD_BUCKETS not configured"),
+        )
+        if bucket not in s3_buckets:
+            logger.debug(f"Bucket '{bucket}' not in ALLOWED_DATA_UPLOAD_BUCKETS config")
+            raise Forbidden(f"Uploading to bucket '{bucket}' is not allowed")
 
     response = {
         "guid": blank_index.guid,
         "url": blank_index.make_signed_url(
-            file_name=params["file_name"], protocol=protocol, expires_in=expires_in
+            file_name=params["file_name"],
+            protocol=protocol,
+            expires_in=expires_in,
+            bucket=bucket,
         ),
     }
 
@@ -193,6 +206,9 @@ def upload_data_file():
 def init_multipart_upload():
     """
     Initialize a multipart upload request
+
+    NOTE This endpoint does not currently accept a `bucket` parameter like
+    `POST /upload` and `GET /upload/<GUID>` do.
     """
     params = flask.request.get_json()
     if not params:
@@ -293,7 +309,20 @@ def upload_file(file_id):
         file_name = str(file_id).replace("/", "_")
         logger.warning(f"file_name not provided, using '{file_name}'")
 
-    result = get_signed_url_for_file("upload", file_id, file_name=file_name)
+    bucket = flask.request.args.get("bucket")
+    if bucket:
+        s3_buckets = get_value(
+            flask.current_app.config,
+            "ALLOWED_DATA_UPLOAD_BUCKETS",
+            InternalError("ALLOWED_DATA_UPLOAD_BUCKETS not configured"),
+        )
+        if bucket not in s3_buckets:
+            logger.debug(f"Bucket '{bucket}' not in ALLOWED_DATA_UPLOAD_BUCKETS config")
+            raise Forbidden(f"Uploading to bucket '{bucket}' is not allowed")
+
+    result = get_signed_url_for_file(
+        "upload", file_id, file_name=file_name, bucket=bucket
+    )
     return flask.jsonify(result)
 
 

fence/blueprints/data/indexd.py

@@ -73,6 +73,7 @@ def get_signed_url_for_file(
     requested_protocol=None,
     ga4gh_passports=None,
     db_session=None,
+    bucket=None,
 ):
     requested_protocol = requested_protocol or flask.request.args.get("protocol", None)
     r_pays_project = flask.request.args.get("userProject", None)
@@ -144,6 +145,7 @@ def get_signed_url_for_file(
         r_pays_project=r_pays_project,
         file_name=file_name,
         users_from_passports=users_from_passports,
+        bucket=bucket,
     )
 
     # a single user from the list was authorized so update the audit log to reflect that
@@ -258,7 +260,7 @@ def index_document(self):
         )
         return document
 
-    def make_signed_url(self, file_name, protocol=None, expires_in=None):
+    def make_signed_url(self, file_name, protocol=None, expires_in=None, bucket=None):
         """
         Works for upload only; S3 or Azure Blob Storage only
         (only supported case for data upload flow currently).
@@ -286,12 +288,15 @@ def make_signed_url(self, file_name, protocol=None, expires_in=None):
                 "upload", expires_in
             )
         else:
-            try:
-                bucket = flask.current_app.config["DATA_UPLOAD_BUCKET"]
-            except KeyError:
-                raise InternalError(
-                    "fence not configured with data upload bucket; can't create signed URL"
-                )
+            if not bucket:
+                try:
+                    bucket = flask.current_app.config["DATA_UPLOAD_BUCKET"]
+                except KeyError:
+                    raise InternalError(
+                        "fence not configured with data upload bucket; can't create signed URL"
+                    )
+
+            self.logger.debug("Attemping to upload to bucket '{}'".format(bucket))
             s3_url = "s3://{}/{}/{}".format(bucket, self.guid, file_name)
             url = S3IndexedFileLocation(s3_url).get_signed_url("upload", expires_in)
 
@@ -450,6 +455,7 @@ def get_signed_url(
         r_pays_project=None,
         file_name=None,
         users_from_passports=None,
+        bucket=None,
     ):
         users_from_passports = users_from_passports or {}
         authorized_user = None
@@ -497,6 +503,7 @@ def get_signed_url(
                 r_pays_project,
                 file_name,
                 authorized_user,
+                bucket,
             ),
             authorized_user,
         )
@@ -510,14 +517,18 @@ def _get_signed_url(
         r_pays_project,
         file_name,
         authorized_user=None,
+        bucket=None,
     ):
         if action == "upload":
             # NOTE: self.index_document ensures the GUID exists in indexd and raises
             #       an error if not (which is expected to be caught upstream in the
             #       app)
             blank_record = BlankIndex(uploader="", guid=self.index_document.get("did"))
             return blank_record.make_signed_url(
-                protocol=protocol, file_name=file_name, expires_in=expires_in
+                protocol=protocol,
+                file_name=file_name,
+                expires_in=expires_in,
+                bucket=bucket,
             )
 
         if not protocol:
@@ -876,7 +887,7 @@ def bucket_name(self):
         s3_buckets = get_value(
             flask.current_app.config,
             "S3_BUCKETS",
-            InternalError("buckets not configured"),
+            InternalError("S3_BUCKETS not configured"),
         )
         for bucket in s3_buckets:
             if re.match("^" + bucket + "$", self.parsed_url.netloc):
@@ -892,7 +903,7 @@ def get_credential_to_access_bucket(
         cls, bucket_name, aws_creds, expires_in, boto=None
     ):
         s3_buckets = get_value(
-            config, "S3_BUCKETS", InternalError("buckets not configured")
+            config, "S3_BUCKETS", InternalError("S3_BUCKETS not configured")
         )
         if len(aws_creds) == 0 and len(s3_buckets) == 0:
             raise InternalError("no bucket is configured")
@@ -901,7 +912,8 @@ def get_credential_to_access_bucket(
 
         bucket_cred = s3_buckets.get(bucket_name)
         if bucket_cred is None:
-            raise Unauthorized("permission denied for bucket")
+            logger.debug(f"Bucket '{bucket_name}' not found in S3_BUCKETS config")
+            raise InternalError("permission denied for bucket")
 
         cred_key = get_value(
             bucket_cred, "cred", InternalError("credential of that bucket is missing")
@@ -930,7 +942,7 @@ def get_credential_to_access_bucket(
 
     def get_bucket_region(self):
         s3_buckets = get_value(
-            config, "S3_BUCKETS", InternalError("buckets not configured")
+            config, "S3_BUCKETS", InternalError("S3_BUCKETS not configured")
         )
         if len(s3_buckets) == 0:
             return None
@@ -957,7 +969,7 @@ def get_signed_url(
             config, "AWS_CREDENTIALS", InternalError("credentials not configured")
         )
         s3_buckets = get_value(
-            config, "S3_BUCKETS", InternalError("buckets not configured")
+            config, "S3_BUCKETS", InternalError("S3_BUCKETS not configured")
         )
 
         bucket_name = self.bucket_name()

fence/config-default.yaml

@@ -633,10 +633,13 @@ S3_BUCKETS: {}
 #     region: 'us-east-1'
 #     role-arn: 'arn:aws:iam::role1'
 
-# `DATA_UPLOAD_BUCKET` specifies an S3 bucket to which data files are uploaded,
-# using the `/data/upload` endpoint. This must be one of the first keys under
-# `S3_BUCKETS` (since these are the buckets fence has credentials for).
-DATA_UPLOAD_BUCKET: 'bucket1'
+# Names of the S3 buckets to which data files can be uploaded. They should be
+# configured in `S3_BUCKETS`.
+ALLOWED_DATA_UPLOAD_BUCKETS: []
+
+# Default S3 bucket to which data files are uploaded, when the bucket is not specified
+# by the uploader. It should be configured in `S3_BUCKETS`.
+DATA_UPLOAD_BUCKET: ''
 
 # //////////////////////////////////////////////////////////////////////////////////////
 # PROXY

fence/resources/audit/client.py

@@ -38,7 +38,7 @@ def __init__(self, service_url, logger):
 
         if self.push_type == "aws_sqs":
             aws_sqs_config = config["PUSH_AUDIT_LOGS_CONFIG"]["aws_sqs_config"]
-            # we know the cred is in AWS_CREDENTIALS (see `_check_aws_creds_and_region`)
+            # we know the cred is in AWS_CREDENTIALS (see `_check_buckets_aws_creds_and_region`)
             aws_creds = (
                 config.get("AWS_CREDENTIALS", {})[aws_sqs_config["aws_cred"]]
                 if "aws_cred" in aws_sqs_config