Upgrade Flask and other server python dependencies (#438)

* wip

* wip

* wip

* revert push_tests branch change

Co-authored-by: Mike Lin <mlin@CZIMACOS3726.hawaii.rr.com>
Co-authored-by: atarashansky <atarashansky@chanzuckerberg.com>

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}/<dataset>" + api_version).replace("//", "/"),
             )

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}/<s3_uri>" + 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}/<string:dataset>" + 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(

server/requirements.txt

@@ -1,25 +1,23 @@
 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
 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
 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