From 65ffb05faa5d7931b48a3f2d692b21d9357941a8 Mon Sep 17 00:00:00 2001 From: Mike Lin Date: Thu, 15 Sep 2022 05:15:40 -1000 Subject: [PATCH] Upgrade Flask and other server python dependencies (#438) * wip * wip * wip * revert push_tests branch change Co-authored-by: Mike Lin Co-authored-by: atarashansky --- server/app/api/v2.py | 2 +- server/app/api/v3.py | 6 +++--- server/requirements.txt | 8 +++----- 3 files changed, 7 insertions(+), 9 deletions(-) diff --git a/server/app/api/v2.py b/server/app/api/v2.py index ee4acd40c..f59ad0f48 100644 --- a/server/app/api/v2.py +++ b/server/app/api/v2.py @@ -177,7 +177,7 @@ def register_api_v2(app, app_config, server_config, api_url_prefix): for dataroot_dict in server_config.multi_dataset__dataroot.values(): url_dataroot = dataroot_dict["base_url"] bp_dataroot = Blueprint( - name=f"api_dataset_{url_dataroot}_{api_version}", + name=f"api_dataset_{url_dataroot}_{api_version.replace('.',',')}", import_name=__name__, url_prefix=(f"{api_url_prefix}/{url_dataroot}/" + api_version).replace("//", "/"), ) diff --git a/server/app/api/v3.py b/server/app/api/v3.py index 36a399aff..641c8d950 100644 --- a/server/app/api/v3.py +++ b/server/app/api/v3.py @@ -199,7 +199,7 @@ def register_api_v3(app, app_config, server_config, api_url_prefix): s3uri_api_path = "s3_uri" bp_s3uri = Blueprint( - f"api_dataset_{s3uri_api_path}_{api_version}", + f"api_dataset_{s3uri_api_path}_{api_version.replace('.',',')}", __name__, url_prefix=(f"{api_url_prefix}/{s3uri_api_path}/" + api_version).replace("//", "/"), ) @@ -213,7 +213,7 @@ def register_api_v3(app, app_config, server_config, api_url_prefix): for dataroot_dict in server_config.multi_dataset__dataroot.values(): url_dataroot = dataroot_dict["base_url"] bp_dataroot = Blueprint( - f"api_dataset_{url_dataroot}_{api_version}", + f"api_dataset_{url_dataroot}_{api_version.replace('.',',')}", __name__, url_prefix=(f"{api_url_prefix}/{url_dataroot}/" + api_version).replace("//", "/"), ) @@ -236,7 +236,7 @@ def register_api_v3(app, app_config, server_config, api_url_prefix): # methods=["GET"], # ) else: - bp_api = Blueprint("api", __name__, url_prefix=f"{api_url_prefix}{api_version}") + bp_api = Blueprint("api", __name__, url_prefix=f"{api_url_prefix}{api_version.replace('.',',')}") resources = get_api_dataroot_resources(bp_api) app.register_blueprint(resources.blueprint) app.add_url_rule( diff --git a/server/requirements.txt b/server/requirements.txt index d897f85bf..4a878c12b 100644 --- a/server/requirements.txt +++ b/server/requirements.txt @@ -1,12 +1,11 @@ anndata>=0.7.6 # we need to_memory(), added in 0.7.6 bitarray>=2.3.6 boto3>=1.12.18 -click<8.0,>=5.1 envyaml>=1.9 -Flask>=1.0.2,<2.0.0 # Flask 2.0 is not compatible with the latest version of Flask-RESTful (0.3.8) +Flask~=2.2 Flask-Compress>=1.4.0 Flask-Cors>=3.0.9 # CVE-2020-25032 -Flask-RESTful>=0.3.6 +Flask-RESTful>=0.3.9 flask-server-timing>=0.1.2 flask-talisman>=0.7.0 flatbuffers>=1.11.0,<2.0.0 # cellxgene is not compatible with 2.0.0. Requires migration @@ -14,7 +13,7 @@ flatten-dict>=0.2.0 fsspec>=0.4.4,<0.8.0 gunicorn>=20.0.4 numba>=0.51.2 -numpy<1.21,>=1.17 +numpy>=1.17 packaging>=20.0 pandas>=1.0,!=1.1 # pandas 1.1 breaks tests, https://github.com/pandas-dev/pandas/issues/35446 PyYAML>=5.4 # CVE-2020-14343 @@ -22,4 +21,3 @@ scipy>=1.4 requests>=2.22.0 tiledb==0.16.5 # Explorer's major/minor tiledb version should always be the >= Portal's tiledb major/minor version (for read/write compatibility) s3fs==0.4.2 -MarkupSafe==1.1.1