From c06e267b3adf6c858136255353805b95fdea0967 Mon Sep 17 00:00:00 2001 From: Douglas Rioux Date: Wed, 17 May 2023 15:22:43 -0400 Subject: [PATCH 1/8] Create base class for item models --- snovault/item_models.py | 73 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 73 insertions(+) create mode 100644 snovault/item_models.py diff --git a/snovault/item_models.py b/snovault/item_models.py new file mode 100644 index 000000000..267c28e5b --- /dev/null +++ b/snovault/item_models.py @@ -0,0 +1,73 @@ +from dataclass import dataclass, field +from typing import Any, Optional, Union + +import structlog +from pyramid.request import Request + +from dcicutils.item_models import JsonObject, PortalItem as PortalItemWithoutRequests + + +logger = structlog.getLogger(__name__) + + +@dataclass(frozen=True) +class PortalItem(PortalItemWithoutRequests): + + request: Optional[Request] = field(default=None, hash=False) + + def get_request(self) -> Union[Request, None]: + return self.request + + @classmethod + def from_properties( + cls, properties: JsonObject, embed_items=False, auth=None, request=None, **kwargs: Any + ) -> "PortalItem": + return cls( + properties=properties, embed_items=embed_items, auth=auth, request=request + ) + + @classmethod + def from_identifier_and_existing_item( + cls, identifier: str, existing_item: "PortalItem", **kwargs: Any + ) -> "PortalItem": + embed_items = existing_item.do_embeds() + auth = existing_item.get_auth() + request = existing_item.get_request() + if auth: + return cls.from_identifier_and_auth( + identifier, auth, embed_items=embed_items, **kwargs + ) + if request: + return cls.from_identifier_and_request( + identifier, request, embed_items=embed_items, **kwargs + ) + raise ValueError("Unable to create item from existing item") + + @classmethod + def from_properties_and_existing_item( + cls, properties: JsonObject, existing_item: "PortalItem", **kwargs: Any + ) -> "PortalItem": + embed_items = existing_item.do_embeds() + auth = existing_item.get_auth() + request = existing_item.get_request() + return cls.from_properties( + properties, embed_items=embed_items, auth=auth, request=request, **kwargs + ) + + @classmethod + def from_identifier_and_request( + cls, identifier: str, request: Request, embed_items: bool, **kwargs: Any + ) -> "PortalItem": + properties = cls._get_item_via_request(identifier, request) + return cls.from_properties( + properties=properties, request=request, embed_items=embed_items, **kwargs + ) + + @classmethod + def _get_item_via_request(cls, identifier: str, request: Request) -> JsonObject: + try: + result = request.embed(identifier, "@@object") + except Exception as e: + logger.exception(f"Unable to embed identifer {identifier}: {e}") + result = {} + return result From af5e824e604ba48932caadb5b14d11c467f8e629 Mon Sep 17 00:00:00 2001 From: Douglas Rioux Date: Mon, 17 Jul 2023 15:24:45 -0400 Subject: [PATCH 2/8] Tidy up + add tests --- poetry.lock | 1962 ++++++++++++++-------------- pyproject.toml | 2 +- snovault/item_models.py | 53 +- snovault/tests/test_item_models.py | 108 ++ 4 files changed, 1153 insertions(+), 972 deletions(-) create mode 100644 snovault/tests/test_item_models.py diff --git a/poetry.lock b/poetry.lock index 80d6181fe..def6c9910 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,24 +1,17 @@ -# This file is automatically @generated by Poetry 1.4.0 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand. 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description = "Backported and Experimental Type Hints for Python 3.7+" category = "main" optional = false python-versions = ">=3.7" files = [ - {file = "typing_extensions-4.5.0-py3-none-any.whl", hash = "sha256:fb33085c39dd998ac16d1431ebc293a8b3eedd00fd4a32de0ff79002c19511b4"}, - {file = "typing_extensions-4.5.0.tar.gz", hash = "sha256:5cb5f4a79139d699607b3ef622a1dedafa84e115ab0024e0d9c044a9479ca7cb"}, + {file = "typing_extensions-4.7.1-py3-none-any.whl", hash = "sha256:440d5dd3af93b060174bf433bccd69b0babc3b15b1a8dca43789fd7f61514b36"}, + {file = "typing_extensions-4.7.1.tar.gz", hash = "sha256:b75ddc264f0ba5615db7ba217daeb99701ad295353c45f9e95963337ceeeffb2"}, ] [[package]] name = "urllib3" -version = "1.26.15" +version = "1.26.16" description = "HTTP library with thread-safe connection pooling, file post, and more." category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" files = [ - {file = "urllib3-1.26.15-py2.py3-none-any.whl", hash = "sha256:aa751d169e23c7479ce47a0cb0da579e3ede798f994f5816a74e4f4500dcea42"}, - {file = "urllib3-1.26.15.tar.gz", hash = "sha256:8a388717b9476f934a21484e8c8e61875ab60644d29b9b39e11e4b9dc1c6b305"}, + {file = "urllib3-1.26.16-py2.py3-none-any.whl", hash = "sha256:8d36afa7616d8ab714608411b4a3b13e58f463aee519024578e062e141dce20f"}, + {file = "urllib3-1.26.16.tar.gz", hash = "sha256:8f135f6502756bde6b2a9b28989df5fbe87c9970cecaa69041edcce7f0589b14"}, ] [package.extras] @@ -2700,14 +2764,14 @@ testing = ["coverage", "pytest (>=3.1.0)", "pytest-cov", "pytest-xdist"] [[package]] name = "websocket-client" -version = "1.5.1" +version = "1.6.1" description = "WebSocket client for Python with low level API options" category = "main" optional = false python-versions = ">=3.7" files = [ - {file = "websocket-client-1.5.1.tar.gz", hash = "sha256:3f09e6d8230892547132177f575a4e3e73cfdf06526e20cc02aa1c3b47184d40"}, - {file = "websocket_client-1.5.1-py3-none-any.whl", hash = "sha256:cdf5877568b7e83aa7cf2244ab56a3213de587bbe0ce9d8b9600fc77b455d89e"}, + {file = "websocket-client-1.6.1.tar.gz", hash = "sha256:c951af98631d24f8df89ab1019fc365f2227c0892f12fd150e935607c79dd0dd"}, + {file = "websocket_client-1.6.1-py3-none-any.whl", hash = "sha256:f1f9f2ad5291f0225a49efad77abf9e700b6fef553900623060dad6e26503b9d"}, ] [package.extras] @@ -2739,36 +2803,36 @@ tests = ["PasteDeploy", "WSGIProxy2", "coverage", "mock", "nose (<1.3.0)", "pyqu [[package]] name = "werkzeug" -version = "2.2.3" +version = "2.3.6" description = "The comprehensive WSGI web application library." category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "Werkzeug-2.2.3-py3-none-any.whl", hash = "sha256:56433961bc1f12533306c624f3be5e744389ac61d722175d543e1751285da612"}, - {file = "Werkzeug-2.2.3.tar.gz", hash = "sha256:2e1ccc9417d4da358b9de6f174e3ac094391ea1d4fbef2d667865d819dfd0afe"}, + {file = "Werkzeug-2.3.6-py3-none-any.whl", hash = "sha256:935539fa1413afbb9195b24880778422ed620c0fc09670945185cce4d91a8890"}, + {file = "Werkzeug-2.3.6.tar.gz", hash = "sha256:98c774df2f91b05550078891dee5f0eb0cb797a522c757a2452b9cee5b202330"}, ] [package.dependencies] MarkupSafe = ">=2.1.1" [package.extras] -watchdog = ["watchdog"] +watchdog = ["watchdog (>=2.3)"] [[package]] name = "wheel" -version = "0.38.4" +version = "0.40.0" description = "A built-package format for Python" category = "dev" optional = false python-versions = ">=3.7" files = [ - {file = "wheel-0.38.4-py3-none-any.whl", hash = "sha256:b60533f3f5d530e971d6737ca6d58681ee434818fab630c83a734bb10c083ce8"}, - {file = "wheel-0.38.4.tar.gz", hash = "sha256:965f5259b566725405b05e7cf774052044b1ed30119b5d586b2703aafe8719ac"}, + {file = "wheel-0.40.0-py3-none-any.whl", hash = "sha256:d236b20e7cb522daf2390fa84c55eea81c5c30190f90f29ae2ca1ad8355bf247"}, + {file = "wheel-0.40.0.tar.gz", hash = "sha256:cd1196f3faee2b31968d626e1731c94f99cbdb67cf5a46e4f5656cbee7738873"}, ] [package.extras] -test = ["pytest (>=3.0.0)"] +test = ["pytest (>=6.0.0)"] [[package]] name = "wsgiproxy2" @@ -2906,4 +2970,4 @@ test = ["zope.testing"] [metadata] lock-version = "2.0" python-versions = ">=3.8.1,<3.9" -content-hash = "21d521b5b50ee7b74f714dd34988dbbf1fcba2add428d731dd7f2749aaac24dd" +content-hash = "7d87925e65a027cf4367bdeea228af42d8a4bed39d7d5dd96baef75d6819b47a" diff --git a/pyproject.toml b/pyproject.toml index cef99540f..f95e91395 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -44,7 +44,7 @@ botocore = ">=1.27.36" # no particular version required, but this speeds up sea boto3 = ">=1.24.36" # no particular version required, but this speeds up search elasticsearch = "7.13.4" # versions >= 7.14.0 lock out AWS ES elasticsearch_dsl = "^7.4.0" -dcicutils = "^6.10.0" +dcicutils = {path = "../utils", develop = true} future = ">=0.15.2,<1" html5lib = ">=1.1" # experimental, should be OK now that we're not using moto server humanfriendly = "^1.44.9" diff --git a/snovault/item_models.py b/snovault/item_models.py index 267c28e5b..e15e136a0 100644 --- a/snovault/item_models.py +++ b/snovault/item_models.py @@ -1,10 +1,15 @@ -from dataclass import dataclass, field +from __future__ import annotations + +from dataclasses import dataclass, field from typing import Any, Optional, Union import structlog from pyramid.request import Request -from dcicutils.item_models import JsonObject, PortalItem as PortalItemWithoutRequests +from dcicutils.item_model_utils import ( + JsonObject, + PortalItem as PortalItemWithoutRequests, +) logger = structlog.getLogger(__name__) @@ -12,7 +17,6 @@ @dataclass(frozen=True) class PortalItem(PortalItemWithoutRequests): - request: Optional[Request] = field(default=None, hash=False) def get_request(self) -> Union[Request, None]: @@ -20,47 +24,52 @@ def get_request(self) -> Union[Request, None]: @classmethod def from_properties( - cls, properties: JsonObject, embed_items=False, auth=None, request=None, **kwargs: Any - ) -> "PortalItem": - return cls( - properties=properties, embed_items=embed_items, auth=auth, request=request - ) + cls, + properties: JsonObject, + fetch_links=False, + auth=None, + request=None, + **kwargs: Any, + ) -> PortalItem: + return cls(properties, fetch_links=fetch_links, auth=auth, request=request) @classmethod def from_identifier_and_existing_item( - cls, identifier: str, existing_item: "PortalItem", **kwargs: Any - ) -> "PortalItem": - embed_items = existing_item.do_embeds() + cls, identifier: str, existing_item: PortalItem, **kwargs: Any + ) -> PortalItem: + fetch_links = existing_item.should_fetch_links() auth = existing_item.get_auth() request = existing_item.get_request() if auth: return cls.from_identifier_and_auth( - identifier, auth, embed_items=embed_items, **kwargs + identifier, auth, fetch_links=fetch_links, **kwargs ) if request: return cls.from_identifier_and_request( - identifier, request, embed_items=embed_items, **kwargs + identifier, request, fetch_links=fetch_links, **kwargs ) - raise ValueError("Unable to create item from existing item") + raise RuntimeError( + "Unable to fetch given identifier without auth key or request" + ) @classmethod def from_properties_and_existing_item( - cls, properties: JsonObject, existing_item: "PortalItem", **kwargs: Any - ) -> "PortalItem": - embed_items = existing_item.do_embeds() + cls, properties: JsonObject, existing_item: PortalItem, **kwargs: Any + ) -> PortalItem: + fetch_links = existing_item.should_fetch_links() auth = existing_item.get_auth() request = existing_item.get_request() return cls.from_properties( - properties, embed_items=embed_items, auth=auth, request=request, **kwargs + properties, fetch_links=fetch_links, auth=auth, request=request, **kwargs ) @classmethod def from_identifier_and_request( - cls, identifier: str, request: Request, embed_items: bool, **kwargs: Any - ) -> "PortalItem": + cls, identifier: str, request: Request, fetch_links: bool, **kwargs: Any + ) -> PortalItem: properties = cls._get_item_via_request(identifier, request) return cls.from_properties( - properties=properties, request=request, embed_items=embed_items, **kwargs + properties, request=request, fetch_links=fetch_links, **kwargs ) @classmethod @@ -68,6 +77,6 @@ def _get_item_via_request(cls, identifier: str, request: Request) -> JsonObject: try: result = request.embed(identifier, "@@object") except Exception as e: - logger.exception(f"Unable to embed identifer {identifier}: {e}") + logger.exception(f"Unable to fetch identifer {identifier}: {e}") result = {} return result diff --git a/snovault/tests/test_item_models.py b/snovault/tests/test_item_models.py new file mode 100644 index 000000000..24980cebd --- /dev/null +++ b/snovault/tests/test_item_models.py @@ -0,0 +1,108 @@ +from contextlib import contextmanager +from typing import Iterator, Optional, Union +from unittest import mock + +import pytest +from dcicutils.item_model_utils import JsonObject +from dcicutils.testing_utils import patch_context +from pyramid.request import Request + +from .. import item_models as item_models_module +from ..item_models import PortalItem + + +SOME_UUID = "uuid1234" +SOME_ITEM_PROPERTIES = { + "uuid": SOME_UUID, +} +SOME_AUTH = {"key": "some_key", "secret": "some_secret"} + + +@contextmanager +def patch_from_identifier_and_auth(**kwargs) -> Iterator[mock.MagicMock]: + with patch_context( + item_models_module.PortalItem.from_identifier_and_auth, **kwargs + ) as mock_item: + yield mock_item + + +@contextmanager +def patch_from_identifier_and_request(**kwargs) -> Iterator[mock.MagicMock]: + with patch_context( + item_models_module.PortalItem.from_identifier_and_request, **kwargs + ) as mock_item: + yield mock_item + + +def mock_request(embed_exception: bool = False) -> mock.MagicMock: + result = mock.create_autospec(Request, instance=True) + embed_method = mock.MagicMock() + if embed_exception: + embed_method.side_effect = Exception + result.embed = embed_method + return result + + +def get_portal_item( + auth: Optional[JsonObject] = SOME_AUTH, + fetch_links: bool = False, + request: Optional[Request] = None, +) -> PortalItem: + return PortalItem({}, auth=auth, fetch_links=fetch_links, request=request) + + +class TestPortalItem: + @pytest.mark.parametrize( + "auth,request_param,exception_expected", + [ + (None, None, True), + (SOME_AUTH, None, False), + (None, mock_request(), False), + (SOME_AUTH, mock_request(), False), + ], + ) + def test_from_identifier_and_existing_item( + self, + auth: Union[JsonObject, None], + request_param: Union[Request, None], + exception_expected: bool, + ) -> None: + identifier = SOME_UUID + fetch_links = True + portal_item = get_portal_item( + fetch_links=fetch_links, auth=auth, request=request_param + ) + with patch_from_identifier_and_auth() as mock_from_identifier_and_auth: + with patch_from_identifier_and_request() as mock_from_identifier_and_request: + if exception_expected: + with pytest.raises(RuntimeError): + PortalItem.from_identifier_and_existing_item( + identifier, portal_item + ) + else: + result = PortalItem.from_identifier_and_existing_item( + identifier, portal_item + ) + if auth: + assert result == mock_from_identifier_and_auth.return_value + mock_from_identifier_and_auth.assert_called_once_with( + identifier, auth, fetch_links=fetch_links + ) + mock_from_identifier_and_request.assert_not_called() + elif request_param: + assert result == mock_from_identifier_and_request.return_value + mock_from_identifier_and_request.assert_called_once_with( + identifier, request_param, fetch_links=fetch_links + ) + mock_from_identifier_and_auth.assert_not_called() + + @pytest.mark.parametrize("exception_expected", [True, False]) + def test_get_item_via_request(self, exception_expected: bool) -> None: + identifier = SOME_UUID + request = mock_request(embed_exception=exception_expected) + result = PortalItem._get_item_via_request(identifier, request) + request.embed.assert_called_once_with(identifier, "@@object") + if exception_expected: + assert result == {} + else: + assert result == request.embed.return_value From 238ec5aa1ffcae13be0b707f2b5580370795f2c2 Mon Sep 17 00:00:00 2001 From: William Ronchetti Date: Thu, 20 Jul 2023 16:03:57 -0400 Subject: [PATCH 3/8] version --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index f95e91395..fd9074f08 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "dcicsnovault" -version = "7.3.0" +version = "7.3.0.0b0" description = "Storage support for 4DN Data Portals." authors = ["4DN-DCIC Team "] license = "MIT" From 8439ffb363b3c06176f4239a69fea1072fc8f03b Mon Sep 17 00:00:00 2001 From: William Ronchetti Date: Thu, 20 Jul 2023 16:04:41 -0400 Subject: [PATCH 4/8] version again --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index fd9074f08..db829a722 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "dcicsnovault" -version = "7.3.0.0b0" +version = "7.3.0.0b1" description = "Storage support for 4DN Data Portals." authors = ["4DN-DCIC Team "] license = "MIT" From e9f2ac9a3c33141b837c476169a3c9c9b8486064 Mon Sep 17 00:00:00 2001 From: William Ronchetti Date: Thu, 20 Jul 2023 16:08:15 -0400 Subject: [PATCH 5/8] version again with proper utils --- poetry.lock | 46 ++++++++++++++++++++++------------------------ pyproject.toml | 2 +- 2 files changed, 23 insertions(+), 25 deletions(-) diff --git a/poetry.lock b/poetry.lock index def6c9910..4d4bfcab2 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand. +# This file is automatically @generated by Poetry and should not be changed by hand. [[package]] name = "async-timeout" @@ -813,39 +813,37 @@ test-randomorder = ["pytest-randomly"] [[package]] name = "dcicutils" -version = "7.5.2" +version = "7.6.0" description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources" category = "main" optional = false python-versions = ">=3.7,<3.10" -files = [] -develop = true +files = [ + {file = "dcicutils-7.6.0-py3-none-any.whl", hash = "sha256:043d700aab91cc20b08acad07948eeafde21504d0fcc37813bc82cc220e28889"}, + {file = "dcicutils-7.6.0.tar.gz", hash = "sha256:2944c40c907d26154ad1865b52434b52c66e12b548938f90fe32b061d81d380f"}, +] [package.dependencies] aws-requests-auth = ">=0.4.2,<1" -boto3 = "^1.17.39" -botocore = "^1.20.39" -docker = "^4.4.4" +boto3 = ">=1.17.39,<2.0.0" +botocore = ">=1.20.39,<2.0.0" +docker = ">=4.4.4,<5.0.0" elasticsearch = "7.13.4" -gitpython = "^3.1.2" -opensearch-py = "^2.0.1" -PyJWT = "^2.6.0" -pyOpenSSL = "^23.1.1" +gitpython = ">=3.1.2,<4.0.0" +opensearch-py = ">=2.0.1,<3.0.0" +PyJWT = ">=2.6.0,<3.0.0" +pyOpenSSL = ">=23.1.1,<24.0.0" pytz = ">=2020.4" PyYAML = ">=5.1,<5.5" -redis = "^4.5.1" -requests = "^2.21.0" -rfc3986 = "^1.4.0" -structlog = "^19.2.0" +redis = ">=4.5.1,<5.0.0" +requests = ">=2.21.0,<3.0.0" +rfc3986 = ">=1.4.0,<2.0.0" +structlog = ">=19.2.0,<20.0.0" toml = ">=0.10.1,<1" -tqdm = "^4.65.0" +tqdm = ">=4.65.0,<5.0.0" typing-extensions = ">=3.8" -urllib3 = "^1.26.6" -webtest = "^2.0.34" - -[package.source] -type = "directory" -url = "../utils" +urllib3 = ">=1.26.6,<2.0.0" +webtest = ">=2.0.34,<3.0.0" [[package]] name = "docker" @@ -2493,7 +2491,7 @@ files = [ ] [package.dependencies] -greenlet = {version = "!=0.4.17", markers = "python_version >= \"3\" and platform_machine == \"aarch64\" or python_version >= \"3\" and platform_machine == \"ppc64le\" or python_version >= \"3\" and platform_machine == \"x86_64\" or python_version >= \"3\" and platform_machine == \"amd64\" or python_version >= \"3\" and platform_machine == \"AMD64\" or python_version >= \"3\" and platform_machine == \"win32\" or python_version >= \"3\" and platform_machine == \"WIN32\""} +greenlet = {version = "!=0.4.17", markers = "python_version >= \"3\" and (platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\")"} [package.extras] aiomysql = ["aiomysql", "greenlet (!=0.4.17)"] @@ -2970,4 +2968,4 @@ test = ["zope.testing"] [metadata] lock-version = "2.0" python-versions = ">=3.8.1,<3.9" -content-hash = "7d87925e65a027cf4367bdeea228af42d8a4bed39d7d5dd96baef75d6819b47a" +content-hash = "f9931dba10353b1b806e930eaed79455a2ea59dea9d1911c8b7ad7024689cbab" diff --git a/pyproject.toml b/pyproject.toml index db829a722..ed270d86a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -44,7 +44,7 @@ botocore = ">=1.27.36" # no particular version required, but this speeds up sea boto3 = ">=1.24.36" # no particular version required, but this speeds up search elasticsearch = "7.13.4" # versions >= 7.14.0 lock out AWS ES elasticsearch_dsl = "^7.4.0" -dcicutils = {path = "../utils", develop = true} +dcicutils = "^7.5.0" future = ">=0.15.2,<1" html5lib = ">=1.1" # experimental, should be OK now that we're not using moto server humanfriendly = "^1.44.9" From 4114315157a49a03b01b9385281d12a5af37386e Mon Sep 17 00:00:00 2001 From: Douglas Rioux Date: Wed, 26 Jul 2023 11:17:12 -0400 Subject: [PATCH 6/8] Bring in utils beta + bump beta version --- poetry.lock | 87 +++++++++++++++++++++++++------------------------- pyproject.toml | 4 +-- 2 files changed, 46 insertions(+), 45 deletions(-) diff --git a/poetry.lock b/poetry.lock index 4d4bfcab2..80c8686c2 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry and should not be changed by hand. +# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand. [[package]] name = "async-timeout" @@ -48,18 +48,18 @@ lxml = ["lxml"] [[package]] name = "boto3" -version = "1.28.3" +version = "1.28.11" description = "The AWS SDK for Python" category = "main" optional = false python-versions = ">= 3.7" files = [ - {file = "boto3-1.28.3-py3-none-any.whl", hash = "sha256:34f07b3fc2503240c0f58114cf3afea91295c7996d084991b78a278a56157c48"}, - {file = "boto3-1.28.3.tar.gz", hash = "sha256:610369a7f984b58973c097ea649ec81976c04565d39a2d6d3edc280d23b0cb87"}, + {file = "boto3-1.28.11-py3-none-any.whl", hash = "sha256:e24460d50001b517c6734dcf1c879feb43aa2062d88d9bdbb8703c986cb05941"}, + {file = "boto3-1.28.11.tar.gz", hash = "sha256:0fe7a35cf0041145c8eefebd3ae2ddf41baed62d7c963e5042b8ed8c297f648f"}, ] [package.dependencies] -botocore = ">=1.31.3,<1.32.0" +botocore = ">=1.31.11,<1.32.0" jmespath = ">=0.7.1,<2.0.0" s3transfer = ">=0.6.0,<0.7.0" @@ -68,14 +68,14 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] [[package]] name = "boto3-stubs" -version = "1.28.3.post2" -description = "Type annotations for boto3 1.28.3 generated with mypy-boto3-builder 7.15.0" +version = "1.28.11" +description = "Type annotations for boto3 1.28.11 generated with mypy-boto3-builder 7.15.1" category = "dev" optional = false python-versions = ">=3.7" files = [ - {file = "boto3-stubs-1.28.3.post2.tar.gz", hash = "sha256:649fd1785e268843b4df9c858bdcfd306ef4943f6b31b174af4d7589777b7bf6"}, - {file = "boto3_stubs-1.28.3.post2-py3-none-any.whl", hash = "sha256:00439a9d3180b2e83be050235a0bed860903cb5b003c93fbcac4453e1f926217"}, + {file = "boto3-stubs-1.28.11.tar.gz", hash = "sha256:d571858f4cea37da8d1afb4858c442b3cfbed2e072d3a040fcb86849de2b55ae"}, + {file = "boto3_stubs-1.28.11-py3-none-any.whl", hash = "sha256:ac7e6e89a1102b9f2d6aba86423553e4c692dffb6a1dabfbc5b30aad47d87842"}, ] [package.dependencies] @@ -89,7 +89,7 @@ account = ["mypy-boto3-account (>=1.28.0,<1.29.0)"] acm = ["mypy-boto3-acm (>=1.28.0,<1.29.0)"] acm-pca = ["mypy-boto3-acm-pca (>=1.28.0,<1.29.0)"] alexaforbusiness = ["mypy-boto3-alexaforbusiness (>=1.28.0,<1.29.0)"] -all = ["mypy-boto3-accessanalyzer (>=1.28.0,<1.29.0)", "mypy-boto3-account (>=1.28.0,<1.29.0)", "mypy-boto3-acm (>=1.28.0,<1.29.0)", "mypy-boto3-acm-pca (>=1.28.0,<1.29.0)", "mypy-boto3-alexaforbusiness (>=1.28.0,<1.29.0)", "mypy-boto3-amp (>=1.28.0,<1.29.0)", "mypy-boto3-amplify (>=1.28.0,<1.29.0)", "mypy-boto3-amplifybackend (>=1.28.0,<1.29.0)", "mypy-boto3-amplifyuibuilder (>=1.28.0,<1.29.0)", "mypy-boto3-apigateway (>=1.28.0,<1.29.0)", "mypy-boto3-apigatewaymanagementapi (>=1.28.0,<1.29.0)", "mypy-boto3-apigatewayv2 (>=1.28.0,<1.29.0)", "mypy-boto3-appconfig (>=1.28.0,<1.29.0)", "mypy-boto3-appconfigdata (>=1.28.0,<1.29.0)", "mypy-boto3-appfabric (>=1.28.0,<1.29.0)", "mypy-boto3-appflow (>=1.28.0,<1.29.0)", "mypy-boto3-appintegrations (>=1.28.0,<1.29.0)", "mypy-boto3-application-autoscaling (>=1.28.0,<1.29.0)", "mypy-boto3-application-insights (>=1.28.0,<1.29.0)", 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test-randomorder = ["pytest-randomly"] [[package]] name = "dcicutils" -version = "7.6.0" +version = "7.5.2.1b1" description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources" category = "main" optional = false python-versions = ">=3.7,<3.10" files = [ - {file = "dcicutils-7.6.0-py3-none-any.whl", hash = "sha256:043d700aab91cc20b08acad07948eeafde21504d0fcc37813bc82cc220e28889"}, - {file = "dcicutils-7.6.0.tar.gz", hash = "sha256:2944c40c907d26154ad1865b52434b52c66e12b548938f90fe32b061d81d380f"}, + {file = "dcicutils-7.5.2.1b1-py3-none-any.whl", hash = "sha256:d5bad0191db40859dcef608c47a7f7285ed6e383f6d60f6289335dd0386fec4b"}, + {file = "dcicutils-7.5.2.1b1.tar.gz", hash = "sha256:8af6cf44559ae9e7199d246272425fb29bc554a1a5b1fe7b5419fa2ee14f183f"}, ] [package.dependencies] @@ -1514,19 +1515,19 @@ test = ["docutils", "pytest-cov", "pytest-pycodestyle", "pytest-runner"] [[package]] name = "pipdeptree" -version = "2.10.2" +version = "2.11.0" description = 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"virtualenv (>=20.24,<21)"] [[package]] name = "plaster" @@ -1742,14 +1743,14 @@ files = [ [[package]] name = "pyjwt" -version = "2.7.0" +version = "2.8.0" description = "JSON Web Token implementation in Python" category = "main" optional = false python-versions = ">=3.7" files = [ - {file = "PyJWT-2.7.0-py3-none-any.whl", hash = "sha256:ba2b425b15ad5ef12f200dc67dd56af4e26de2331f965c5439994dad075876e1"}, - {file = "PyJWT-2.7.0.tar.gz", hash = "sha256:bd6ca4a3c4285c1a2d4349e5a035fdf8fb94e04ccd0fcbe6ba289dae9cc3e074"}, + {file = "PyJWT-2.8.0-py3-none-any.whl", hash = "sha256:59127c392cc44c2da5bb3192169a91f429924e17aff6534d70fdc02ab3e04320"}, + {file = "PyJWT-2.8.0.tar.gz", hash = "sha256:57e28d156e3d5c10088e0c68abb90bfac3df82b40a71bd0daa20c65ccd5c23de"}, ] [package.extras] @@ -2491,7 +2492,7 @@ files = [ ] [package.dependencies] -greenlet = {version = "!=0.4.17", markers = "python_version >= \"3\" and (platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\")"} +greenlet = {version = "!=0.4.17", markers = "python_version >= \"3\" and platform_machine == \"aarch64\" or python_version >= \"3\" and platform_machine == \"ppc64le\" or python_version >= \"3\" and platform_machine == \"x86_64\" or python_version >= \"3\" and platform_machine == \"amd64\" or python_version >= \"3\" and platform_machine == \"AMD64\" or python_version >= \"3\" and platform_machine == \"win32\" or python_version >= \"3\" and platform_machine == \"WIN32\""} [package.extras] aiomysql = ["aiomysql", "greenlet (!=0.4.17)"] @@ -2634,26 +2635,26 @@ docs = ["Sphinx (>=1.3.1)", "docutils", "pylons-sphinx-themes"] [[package]] name = "types-awscrt" -version = "0.16.24" +version = "0.16.26" description = "Type annotations and code completion for awscrt" category = "dev" optional = false python-versions = ">=3.7,<4.0" files = [ - {file = "types_awscrt-0.16.24-py3-none-any.whl", hash = "sha256:6cdfc458aca186fb73261895efeba1a2a0f3cf8f63f8b6ef32ec43739a64e4ae"}, - {file = "types_awscrt-0.16.24.tar.gz", hash = "sha256:cd0d4313fac0859a2b406080782076648524840e26780dbd3b5cbd9cc315834a"}, + {file = "types_awscrt-0.16.26-py3-none-any.whl", hash = "sha256:47bcfd741465196e000e5a29ea98516765d2e93803d3fb67f9d6be79a632ee98"}, + {file = "types_awscrt-0.16.26.tar.gz", hash = "sha256:011b0efc054cddb542416f4a38452a3cab3f2d6cef7af0cd124c03a89634f101"}, ] [[package]] name = "types-pyyaml" -version = "6.0.12.10" +version = "6.0.12.11" description = "Typing stubs for PyYAML" category = "dev" optional = false python-versions = "*" files = [ - {file = "types-PyYAML-6.0.12.10.tar.gz", hash = "sha256:ebab3d0700b946553724ae6ca636ea932c1b0868701d4af121630e78d695fc97"}, - {file = "types_PyYAML-6.0.12.10-py3-none-any.whl", hash = "sha256:662fa444963eff9b68120d70cda1af5a5f2aa57900003c2006d7626450eaae5f"}, + {file = "types-PyYAML-6.0.12.11.tar.gz", hash = "sha256:7d340b19ca28cddfdba438ee638cd4084bde213e501a3978738543e27094775b"}, + {file = "types_PyYAML-6.0.12.11-py3-none-any.whl", hash = "sha256:a461508f3096d1d5810ec5ab95d7eeecb651f3a15b71959999988942063bf01d"}, ] [[package]] @@ -2819,18 +2820,18 @@ watchdog = ["watchdog (>=2.3)"] [[package]] name = "wheel" -version = "0.40.0" +version = "0.41.0" description = "A built-package format for Python" category = "dev" optional = false python-versions = ">=3.7" files = [ - {file = "wheel-0.40.0-py3-none-any.whl", hash = "sha256:d236b20e7cb522daf2390fa84c55eea81c5c30190f90f29ae2ca1ad8355bf247"}, - {file = "wheel-0.40.0.tar.gz", hash = "sha256:cd1196f3faee2b31968d626e1731c94f99cbdb67cf5a46e4f5656cbee7738873"}, + {file = "wheel-0.41.0-py3-none-any.whl", hash = "sha256:7e9be3bbd0078f6147d82ed9ed957e323e7708f57e134743d2edef3a7b7972a9"}, + {file = "wheel-0.41.0.tar.gz", hash = "sha256:55a0f0a5a84869bce5ba775abfd9c462e3a6b1b7b7ec69d72c0b83d673a5114d"}, ] [package.extras] -test = ["pytest (>=6.0.0)"] +test = ["pytest (>=6.0.0)", "setuptools (>=65)"] [[package]] name = "wsgiproxy2" @@ -2968,4 +2969,4 @@ test = ["zope.testing"] [metadata] lock-version = "2.0" python-versions = ">=3.8.1,<3.9" -content-hash = "f9931dba10353b1b806e930eaed79455a2ea59dea9d1911c8b7ad7024689cbab" +content-hash = "c260900c13efcd1c51bd4241854fa97e58c9f91d063d354668811d275889b0ec" diff --git a/pyproject.toml b/pyproject.toml index ed270d86a..bffa37e6f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "dcicsnovault" -version = "7.3.0.0b1" +version = "7.3.0.0b2" description = "Storage support for 4DN Data Portals." authors = ["4DN-DCIC Team "] license = "MIT" @@ -44,7 +44,7 @@ botocore = ">=1.27.36" # no particular version required, but this speeds up sea boto3 = ">=1.24.36" # no particular version required, but this speeds up search elasticsearch = "7.13.4" # versions >= 7.14.0 lock out AWS ES elasticsearch_dsl = "^7.4.0" -dcicutils = "^7.5.0" +dcicutils = "7.5.2.1b1" future = ">=0.15.2,<1" html5lib = ">=1.1" # experimental, should be OK now that we're not using moto server humanfriendly = "^1.44.9" From b42abb360935d1a8f9269a8ce04ee73e087fa53c Mon Sep 17 00:00:00 2001 From: Douglas Rioux Date: Thu, 3 Aug 2023 15:45:55 -0400 Subject: [PATCH 7/8] Bring in updated utils beta --- poetry.lock | 169 +++++++++++++++++++++++++------------------------ pyproject.toml | 2 +- 2 files changed, 87 insertions(+), 84 deletions(-) diff --git a/poetry.lock b/poetry.lock index 80c8686c2..907ae797f 100644 --- a/poetry.lock +++ b/poetry.lock @@ -48,18 +48,18 @@ lxml = ["lxml"] [[package]] name = "boto3" -version = "1.28.11" +version = "1.28.19" description = "The AWS SDK for Python" category = "main" optional = false python-versions = ">= 3.7" files = [ - {file = "boto3-1.28.11-py3-none-any.whl", hash = "sha256:e24460d50001b517c6734dcf1c879feb43aa2062d88d9bdbb8703c986cb05941"}, - {file = "boto3-1.28.11.tar.gz", hash = "sha256:0fe7a35cf0041145c8eefebd3ae2ddf41baed62d7c963e5042b8ed8c297f648f"}, + {file = "boto3-1.28.19-py3-none-any.whl", hash = "sha256:1bae3e6222c7272af44ab4dc456fc4cb7d2d7044489b7a4a08f9cd0fbad6d213"}, + {file = "boto3-1.28.19.tar.gz", hash = "sha256:8630c2c38c3130e31e1a4182943aee8bc7dd1a1ad9729092b46fdbc8ac045a77"}, ] [package.dependencies] -botocore = ">=1.31.11,<1.32.0" +botocore = ">=1.31.19,<1.32.0" jmespath = ">=0.7.1,<2.0.0" s3transfer = ">=0.6.0,<0.7.0" @@ -68,14 +68,14 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] [[package]] name = "boto3-stubs" -version = "1.28.11" -description = "Type annotations for boto3 1.28.11 generated with mypy-boto3-builder 7.15.1" +version = "1.28.18" +description = "Type annotations for boto3 1.28.18 generated with mypy-boto3-builder 7.17.1" category = "dev" optional = false python-versions = ">=3.7" files = [ - {file = "boto3-stubs-1.28.11.tar.gz", hash = "sha256:d571858f4cea37da8d1afb4858c442b3cfbed2e072d3a040fcb86849de2b55ae"}, - {file = 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"sha256:ec8b276a6b60bd80defed25add7e439881c19e64850afd9b346283d4165fd0fd"}, + {file = "pyflakes-3.1.0-py2.py3-none-any.whl", hash = "sha256:4132f6d49cb4dae6819e5379898f2b8cce3c5f23994194c24b77d5da2e36f774"}, + {file = "pyflakes-3.1.0.tar.gz", hash = "sha256:a0aae034c444db0071aa077972ba4768d40c830d9539fd45bf4cd3f8f6992efc"}, ] [[package]] @@ -1780,14 +1783,14 @@ test = ["flaky", "pretend", "pytest (>=3.0.1)"] [[package]] name = "pyparsing" -version = "3.1.0" +version = "3.1.1" description = "pyparsing module - Classes and methods to define and execute parsing grammars" category = "main" optional = false python-versions = ">=3.6.8" files = [ - {file = "pyparsing-3.1.0-py3-none-any.whl", hash = "sha256:d554a96d1a7d3ddaf7183104485bc19fd80543ad6ac5bdb6426719d766fb06c1"}, - {file = "pyparsing-3.1.0.tar.gz", hash = "sha256:edb662d6fe322d6e990b1594b5feaeadf806803359e3d4d42f11e295e588f0ea"}, + {file = "pyparsing-3.1.1-py3-none-any.whl", hash = "sha256:32c7c0b711493c72ff18a981d24f28aaf9c1fb7ed5e9667c9e84e3db623bdbfb"}, + {file = "pyparsing-3.1.1.tar.gz", hash = "sha256:ede28a1a32462f5a9705e07aea48001a08f7cf81a021585011deba701581a0db"}, ] [package.extras] @@ -2206,21 +2209,21 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"] [[package]] name = "responses" -version = "0.23.1" +version = "0.23.3" description = "A utility library for mocking out the `requests` Python library." category = "dev" optional = false python-versions = ">=3.7" files = [ - {file = "responses-0.23.1-py3-none-any.whl", hash = "sha256:8a3a5915713483bf353b6f4079ba8b2a29029d1d1090a503c70b0dc5d9d0c7bd"}, - {file = "responses-0.23.1.tar.gz", hash = "sha256:c4d9aa9fc888188f0c673eff79a8dadbe2e75b7fe879dc80a221a06e0a68138f"}, + {file = "responses-0.23.3-py3-none-any.whl", hash = "sha256:e6fbcf5d82172fecc0aa1860fd91e58cbfd96cee5e96da5b63fa6eb3caa10dd3"}, + {file = "responses-0.23.3.tar.gz", hash = "sha256:205029e1cb334c21cb4ec64fc7599be48b859a0fd381a42443cdd600bfe8b16a"}, ] [package.dependencies] pyyaml = "*" -requests = ">=2.22.0,<3.0" +requests = ">=2.30.0,<3.0" types-PyYAML = "*" -urllib3 = ">=1.25.10" +urllib3 = ">=1.25.10,<3.0" [package.extras] tests = ["coverage (>=6.0.0)", "flake8", "mypy", "pytest (>=7.0.0)", "pytest-asyncio", "pytest-cov", "pytest-httpserver", "tomli", "tomli-w", "types-requests"] @@ -2635,14 +2638,14 @@ docs = ["Sphinx (>=1.3.1)", "docutils", "pylons-sphinx-themes"] [[package]] name = "types-awscrt" -version = "0.16.26" +version = "0.17.0" description = "Type annotations and code completion for awscrt" category = "dev" optional = false python-versions = ">=3.7,<4.0" files = [ - {file = "types_awscrt-0.16.26-py3-none-any.whl", hash = "sha256:47bcfd741465196e000e5a29ea98516765d2e93803d3fb67f9d6be79a632ee98"}, - {file = "types_awscrt-0.16.26.tar.gz", hash = "sha256:011b0efc054cddb542416f4a38452a3cab3f2d6cef7af0cd124c03a89634f101"}, + {file = "types_awscrt-0.17.0-py3-none-any.whl", hash = "sha256:278c1a913098e226769cd28dc37643a2f360907353a7e8918e1bcdf93d4e34f2"}, + {file = "types_awscrt-0.17.0.tar.gz", hash = "sha256:4214783a747af900a5f98ec020d52ecae5910b470fd636813637a45b82a97516"}, ] [[package]] @@ -2969,4 +2972,4 @@ test = ["zope.testing"] [metadata] lock-version = "2.0" python-versions = ">=3.8.1,<3.9" -content-hash = "c260900c13efcd1c51bd4241854fa97e58c9f91d063d354668811d275889b0ec" +content-hash = "df40f18ba5b4c2b1d1828e94d4f614a5b88f0cbc1632f0fd70093f6473f875ed" diff --git a/pyproject.toml b/pyproject.toml index bffa37e6f..85a9130d8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -44,7 +44,7 @@ botocore = ">=1.27.36" # no particular version required, but this speeds up sea boto3 = ">=1.24.36" # no particular version required, but this speeds up search elasticsearch = "7.13.4" # versions >= 7.14.0 lock out AWS ES elasticsearch_dsl = "^7.4.0" -dcicutils = "7.5.2.1b1" +dcicutils = "7.7.0.1b1" future = ">=0.15.2,<1" html5lib = ">=1.1" # experimental, should be OK now that we're not using moto server humanfriendly = "^1.44.9" From 60a109813a552ab420e96868b1ab8e9a07a0cf7f Mon Sep 17 00:00:00 2001 From: Douglas Rioux Date: Thu, 3 Aug 2023 15:48:59 -0400 Subject: [PATCH 8/8] Clean up for PR --- snovault/item_models.py | 13 +++++-------- snovault/tests/test_item_models.py | 7 +++---- 2 files changed, 8 insertions(+), 12 deletions(-) diff --git a/snovault/item_models.py b/snovault/item_models.py index e15e136a0..54e0ccc2e 100644 --- a/snovault/item_models.py +++ b/snovault/item_models.py @@ -1,15 +1,12 @@ from __future__ import annotations from dataclasses import dataclass, field -from typing import Any, Optional, Union +from typing import Any, Dict, Optional, Union import structlog from pyramid.request import Request -from dcicutils.item_model_utils import ( - JsonObject, - PortalItem as PortalItemWithoutRequests, -) +from dcicutils.item_model_utils import PortalItem as PortalItemWithoutRequests logger = structlog.getLogger(__name__) @@ -25,7 +22,7 @@ def get_request(self) -> Union[Request, None]: @classmethod def from_properties( cls, - properties: JsonObject, + properties: Dict[str, Any], fetch_links=False, auth=None, request=None, @@ -54,7 +51,7 @@ def from_identifier_and_existing_item( @classmethod def from_properties_and_existing_item( - cls, properties: JsonObject, existing_item: PortalItem, **kwargs: Any + cls, properties: Dict[str, Any], existing_item: PortalItem, **kwargs: Any ) -> PortalItem: fetch_links = existing_item.should_fetch_links() auth = existing_item.get_auth() @@ -73,7 +70,7 @@ def from_identifier_and_request( ) @classmethod - def _get_item_via_request(cls, identifier: str, request: Request) -> JsonObject: + def _get_item_via_request(cls, identifier: str, request: Request) -> Dict[str, Any]: try: result = request.embed(identifier, "@@object") except Exception as e: diff --git a/snovault/tests/test_item_models.py b/snovault/tests/test_item_models.py index 24980cebd..35157545e 100644 --- a/snovault/tests/test_item_models.py +++ b/snovault/tests/test_item_models.py @@ -1,9 +1,8 @@ from contextlib import contextmanager -from typing import Iterator, Optional, Union +from typing import Any, Dict, Iterator, Optional, Union from unittest import mock import pytest -from dcicutils.item_model_utils import JsonObject from dcicutils.testing_utils import patch_context from pyramid.request import Request @@ -44,7 +43,7 @@ def mock_request(embed_exception: bool = False) -> mock.MagicMock: def get_portal_item( - auth: Optional[JsonObject] = SOME_AUTH, + auth: Optional[Dict[str, Any]] = SOME_AUTH, fetch_links: bool = False, request: Optional[Request] = None, ) -> PortalItem: @@ -63,7 +62,7 @@ class TestPortalItem: ) def test_from_identifier_and_existing_item( self, - auth: Union[JsonObject, None], + auth: Union[Dict[str, Any], None], request_param: Union[Request, None], exception_expected: bool, ) -> None: