server update

server/common/rest.py

@@ -294,7 +294,9 @@ def layout_obs_get(request, data_adaptor):
 
     try:
         return make_response(
-            data_adaptor.layout_to_fbs_matrix(fields, data_adaptor.get_spatial()), HTTPStatus.OK, {"Content-Type": "application/octet-stream"}
+            data_adaptor.layout_to_fbs_matrix(fields, data_adaptor.get_spatial()),
+            HTTPStatus.OK,
+            {"Content-Type": "application/octet-stream"},
         )
     except (KeyError, DatasetAccessError) as e:
         return abort_and_log(HTTPStatus.BAD_REQUEST, str(e), include_exc_info=True)
@@ -380,7 +382,7 @@ def summarize_var_helper(request, data_adaptor, key, raw_query):
             HTTPStatus.OK,
             {"Content-Type": "application/octet-stream"},
         )
-    except (ValueError) as e:
+    except ValueError as e:
         return abort(HTTPStatus.NOT_FOUND, description=str(e))
     except (UnsupportedSummaryMethod, FilterError) as e:
         return abort(HTTPStatus.BAD_REQUEST, description=str(e))
@@ -399,6 +401,7 @@ def summarize_var_post(request, data_adaptor):
     key = request.args.get("key", default=None)
     return summarize_var_helper(request, data_adaptor, key, request.get_data())
 
+
 def spatial_image_get(request, data_adaptor):
     import io
     import matplotlib.pyplot
@@ -417,7 +420,9 @@ def spatial_image_get(request, data_adaptor):
         return abort_and_log(HTTPStatus.BAD_REQUEST, "spatial information does not contain images")
 
     if resolution not in spatial[library_id]["images"]:
-        return abort_and_log(HTTPStatus.BAD_REQUEST, f"spatial information does not contain requested resolution '{resolution}'")
+        return abort_and_log(
+            HTTPStatus.BAD_REQUEST, f"spatial information does not contain requested resolution '{resolution}'"
+        )
 
     response_image = io.BytesIO()
     img = spatial[library_id]["images"][resolution]
@@ -425,7 +430,7 @@ def spatial_image_get(request, data_adaptor):
     response_image.seek(0)
 
     try:
-        return send_file(response_image, attachment_filename=f"{library_id}-{resolution}.png", mimetype="image/png")
+        return send_file(response_image, download_name=f"{library_id}-{resolution}.png", mimetype="image/png")
     except (KeyError, DatasetAccessError) as e:
         return abort_and_log(HTTPStatus.BAD_REQUEST, str(e), include_exc_info=True)
     except PrepareError:

server/requirements.txt

@@ -1,171 +1,25 @@
-alembic==1.4.2
+# NOTE: If you update 'anndata' min version, also update the 'anndata_version'
-aniso8601==8.0.0
+# matrix value in .github/workflows/compatibility_tests.yml
-anndata==0.8.0
+anndata>=0.7.6 # we need to_memory(), added in 0.7.6
-appdirs==1.4.4
+boto3>=1.12.18
-astroid==2.4.2
+click>=7.1.2
-attrs==19.3.0
-Authlib==0.14.3
-autopep8==1.5.4
-aws-sam-translator==1.25.0
-aws-xray-sdk==2.6.0
-bitarray==2.7.3
-black==23.12.1
-bleach==3.1.5
-boto==2.49.0
-boto3==1.26.94
-botocore==1.29.165
-Brotli==1.0.7
-bump2version==1.0.0
-bumpversion==0.6.0
--e git+git@github.com:chanzuckerberg/cellxgene.git@7d61f47a31a661f49cef6c7d2356228d0aeb044c#egg=cellxgene
-certifi==2020.4.5.1
-cffi==1.14.0
-cfn-lint==0.34.0
-chalice==1.12.0
-chardet==3.0.4
-charset-normalizer==3.3.2
-click==8.1.3
-clickclick==1.2.2
-codecov==2.1.3
-connexion==2.7.0
-contourpy==1.1.1
-coverage==7.4.0
-cryptography==2.9.2
-cycler==0.10.0
-decorator==4.4.2
-docker==4.2.2
-docutils==0.15.2
-ecdsa==0.18.0
-enum-compat==0.0.3
-envyaml==1.10.211231
-fastobo==0.7.2
-flake8==7.0.0
-flake8-black==0.2.0
 Flask==2.2.3
-Flask-Caching==1.8.0
+Flask-Compress>=1.4.0
-Flask-Compress==1.13
+Flask-Cors>=3.0.9  # CVE-2020-25032
-Flask-Cors==3.0.10
+Flask-RESTful>=0.3.6
-Flask-RESTful==0.3.9
+flask-server-timing>=0.1.2
-flask-server-timing==0.1.2
+flask-talisman>=0.7.0
-flask-talisman==1.0.0
+flatbuffers>=1.11.0,<2.0.0 # cellxgene is not compatible with 2.0.0. Requires migration
-flatbuffers==1.12
+flatten-dict>=0.2.0
-flatten-dict==0.4.2
+fsspec>=0.4.4,<0.8.0
-fonttools==4.47.2
+gunicorn>=20.0.4
-fsspec==0.7.4
+h5py>=3.0.0
-furl==2.1.0
+matplotlib>=3.5.0
-future==0.18.2
+numba>=0.51.2
-get-version==2.1
+numpy>=1.17.5
-gevent==23.9.1
+packaging>=20.0
-greenlet==3.0.3
+pandas>=1.0,!=1.1  # pandas 1.1 breaks tests, https://github.com/pandas-dev/pandas/issues/35446
-gunicorn==20.0.4
+PyYAML>=5.4  # CVE-2020-14343
-h5py==3.10.0
+scipy>=1.4
-idna==2.8
+requests>=2.22.0
-importlib-metadata==7.0.1
-importlib-resources==6.1.1
-inflection==0.5.0
-isort==4.3.21
-itsdangerous==2.1.2
-Jinja2==3.1.3
-jmespath==0.10.0
-joblib==0.16.0
-jsondiff==1.1.2
-jsonpatch==1.26
-jsonpickle==1.4.1
-jsonpointer==2.0
-jsonschema==3.2.0
-junit-xml==1.9
-keyring==21.2.1
-kiwisolver==1.2.0
-lazy-object-proxy==1.4.3
-legacy-api-wrap==1.2
-llvmlite==0.39.1
-Mako==1.1.3
-MarkupSafe==2.1.4
-matplotlib==3.7.4
-mccabe==0.7.0
-mock==4.0.2
-more-itertools==8.3.0
-moto==1.3.14
-mypy==1.8.0
-mypy-extensions==0.4.3
-natsort==7.0.1
-networkx==2.4
-numba==0.56.4
-numexpr==2.7.1
-numpy==1.23.5
-openapi-spec-validator==0.2.8
-orderedmultidict==1.0.1
-Owlready2==0.24
-packaging==20.4
-pandas==1.5.3
-parameterized==0.7.4
-pathlib2==2.3.5
-pathspec==0.12.1
-patsy==0.5.1
-Pillow==7.2.0
-pkginfo==1.5.0.1
-platformdirs==4.1.0
-pluggy==0.13.1
-psycopg2-binary==2.8.5
-py==1.8.1
-pyasn1==0.4.8
-pycodestyle==2.11.1
-pycparser==2.20
-pydantic==1.10.6
-pyflakes==3.2.0
-Pygments==2.6.1
-pylint==2.5.3
-PyMySQL==0.9.3
-pyparsing==2.4.7
-pyrsistent==0.16.0
-pytest==5.4.2
-pytest-subtests==0.11.0
-python-dateutil==2.8.1
-python-editor==1.0.4
-python-jose==3.3.0
-python-json-logger==2.0.7
-pytz==2020.1
-PyYAML==6.0.1
-readme-renderer==26.0
-regex==2020.5.14
-requests==2.28.2
-requests-toolbelt==0.9.1
-responses==0.10.15
-rsa==4.9
-s3fs==0.4.2
-s3transfer==0.6.2
-scanpy==1.4.6
-scikit-learn==0.23.2
-scipy==1.10.1
-seaborn==0.10.1
-setuptools-scm==4.1.2
-sinfo==0.3.1
-six==1.15.0
-SQLAlchemy==1.3.19
-sshpubkeys==3.1.0
-statsmodels==0.12.0rc0
-stdlib-list==0.7.0
-swagger-ui-bundle==0.0.6
-tables==3.6.1
-threadpoolctl==2.1.0
-tiledb==0.21.4
-toml==0.10.1
-tomli==2.0.1
-tqdm==4.46.0
-twine==3.1.1
-typed-ast==1.4.1
-types-PyYAML==6.0.12.12
-types-requests==2.31.0.20240106
-types-setuptools==69.0.0.20240115
-typing-extensions==3.7.4.3
-umap-learn==0.4.6
-urllib3==1.25.9
-wcwidth==0.2.2
-webencodings==0.5.1
-websocket-client==0.57.0
 Werkzeug==2.2.3
-wrapt==1.12.1
-xmltodict==0.12.0
-zipp==3.1.0
-zope.event==5.0
-zope.interface==6.1