From 6ee670fa41438cf85b9561997fafaa93383634fc Mon Sep 17 00:00:00 2001 From: William Ronchetti Date: Tue, 19 Mar 2024 11:07:37 -0400 Subject: [PATCH 1/6] add customization for portal health page title --- poetry.lock | 939 +++++++++++++++++------------ pyproject.toml | 1 + snovault/project/health.py | 5 + snovault/project_defs.py | 2 + snovault/root.py | 5 +- snovault/tests/root.py | 2 + snovault/tests/test_health_path.py | 8 + snovault/tests/testappfixtures.py | 1 + 8 files changed, 589 insertions(+), 374 deletions(-) create mode 100644 snovault/project/health.py create mode 100644 snovault/tests/test_health_path.py diff --git a/poetry.lock b/poetry.lock index 912928565..616ac4f4d 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,9 +1,10 @@ -# This file is automatically @generated by Poetry 1.5.1 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 = "arrow" version = "1.3.0" description = "Better dates & times for Python" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -17,12 +18,13 @@ types-python-dateutil = ">=2.8.10" [package.extras] doc = ["doc8", "sphinx (>=7.0.0)", "sphinx-autobuild", "sphinx-autodoc-typehints", "sphinx_rtd_theme (>=1.3.0)"] -test = ["dateparser (==1.*)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (==3.*)"] +test = ["dateparser (>=1.0.0,<2.0.0)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (>=3.0.0,<4.0.0)"] [[package]] name = "async-timeout" version = "4.0.3" description = "Timeout context manager for asyncio programs" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -34,6 +36,7 @@ files = [ name = "attrs" version = "23.2.0" description = "Classes Without Boilerplate" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -53,6 +56,7 @@ tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "p name = "aws-requests-auth" version = "0.4.3" description = "AWS signature version 4 signing process for the python requests module" +category = "main" optional = false python-versions = "*" files = [ @@ -65,35 +69,40 @@ requests = ">=0.14.0" [[package]] name = "beautifulsoup4" -version = "4.12.2" +version = "4.12.3" description = "Screen-scraping library" +category = "main" optional = false python-versions = ">=3.6.0" files = [ - {file = "beautifulsoup4-4.12.2-py3-none-any.whl", hash = "sha256:bd2520ca0d9d7d12694a53d44ac482d181b4ec1888909b035a3dbf40d0f57d4a"}, - {file = "beautifulsoup4-4.12.2.tar.gz", hash = "sha256:492bbc69dca35d12daac71c4db1bfff0c876c00ef4a2ffacce226d4638eb72da"}, + {file = "beautifulsoup4-4.12.3-py3-none-any.whl", hash = "sha256:b80878c9f40111313e55da8ba20bdba06d8fa3969fc68304167741bbf9e082ed"}, + {file = "beautifulsoup4-4.12.3.tar.gz", hash = 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+botocore = ">=1.34.65,<1.35.0" jmespath = ">=0.7.1,<2.0.0" s3transfer = ">=0.10.0,<0.11.0" @@ -102,13 +111,14 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] [[package]] name = "boto3-stubs" -version = "1.34.14" -description = "Type annotations for boto3 1.34.14 generated with mypy-boto3-builder 7.23.0" +version = "1.34.65" +description = "Type annotations for boto3 1.34.65 generated with mypy-boto3-builder 7.23.2" +category = "dev" optional = false python-versions = ">=3.8" files = [ - {file = "boto3-stubs-1.34.14.tar.gz", hash = "sha256:2926f993f6fa8936b7c4dd1552c1eb1618a664657b5db595b23eb7a389666d5e"}, - {file = "boto3_stubs-1.34.14-py3-none-any.whl", hash = "sha256:7c65a73a896ca8482ca6447e2222a2d2bc3b0bc63dbcdce8b809ab3a5eef7ffe"}, + {file = "boto3-stubs-1.34.65.tar.gz", hash = "sha256:105da4a04dcb5e4ddc90f21ab8b24a3423ecfacb4775b8ccd3879574e5dce358"}, + {file = "boto3_stubs-1.34.65-py3-none-any.whl", hash = "sha256:2afd696c8bb4daf8890ecd75a720e1733cd8b8556eaecc92c36f9b56fc6013bd"}, 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python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -3170,6 +3360,7 @@ files = [ name = "xmltodict" version = "0.13.0" description = "Makes working with XML feel like you are working with JSON" +category = "dev" optional = false python-versions = ">=3.4" files = [ @@ -3179,23 +3370,25 @@ files = [ [[package]] name = "zipp" -version = "3.17.0" +version = "3.18.1" description = "Backport of pathlib-compatible object wrapper for zip files" +category = "main" optional = false python-versions = ">=3.8" files = [ - {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"}, - {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"}, + {file = "zipp-3.18.1-py3-none-any.whl", hash = "sha256:206f5a15f2af3dbaee80769fb7dc6f249695e940acca08dfb2a4769fe61e538b"}, + {file = "zipp-3.18.1.tar.gz", hash = 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python-versions = "*" files = [ @@ -3214,6 +3407,7 @@ test = ["zope.testrunner"] name = "zope-interface" version = "5.5.2" description = "Interfaces for Python" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -3267,6 +3461,7 @@ testing = ["coverage (>=5.0.3)", "zope.event", "zope.testing"] name = "zope-sqlalchemy" version = "1.6" description = "Minimal Zope/SQLAlchemy transaction integration" +category = "main" optional = false python-versions = "*" files = [ @@ -3286,4 +3481,4 @@ test = ["zope.testing"] [metadata] lock-version = "2.0" python-versions = ">=3.8.1,<3.12" -content-hash = "2c7ee504d8429761be4db54bdf644193837928042a48de092fc36feff8024902" +content-hash = "ed86146fec6ecbd7dc96b212d0b03b4453cb3ea04de9e17258a390eff0a216e4" diff --git a/pyproject.toml b/pyproject.toml index b1719645e..1b03e0374 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -84,6 +84,7 @@ xlrd = "^1.0.0" "zope.interface" = ">=4.7.2,<6" "zope.sqlalchemy" = "1.6" jsonschema = {extras = ["format-nongpl"], version = "^4.19.0"} +uptime = "^3.0.1" [tool.poetry.dev-dependencies] boto3-stubs = ">=1.28.62" # no particular version required, but this speeds up search diff --git a/snovault/project/health.py b/snovault/project/health.py new file mode 100644 index 000000000..d0d59dd51 --- /dev/null +++ b/snovault/project/health.py @@ -0,0 +1,5 @@ +class SnovaultProjectHealthValue: + + @staticmethod + def get_app_namespace(): + return 'ENCODED' diff --git a/snovault/project_defs.py b/snovault/project_defs.py index fdde27913..292382c00 100644 --- a/snovault/project_defs.py +++ b/snovault/project_defs.py @@ -6,6 +6,7 @@ from .project.loadxl import SnovaultProjectLoadxl from .project.renderers import SnovaultProjectRenderers from .project.schema_views import SnovaultProjectSchemaViews +from .project.health import SnovaultProjectHealthValue @C4ProjectRegistry.register("dcicsnovault") @@ -16,6 +17,7 @@ class SnovaultProject(SnovaultProjectAccessKey, SnovaultProjectLoadxl, SnovaultProjectRenderers, SnovaultProjectSchemaViews, + SnovaultProjectHealthValue, C4Project): NAMES = {"NAME": "snovault", "PYPI_NAME": "dcicsnovault"} ACCESSION_PREFIX = "SNO" diff --git a/snovault/root.py b/snovault/root.py index 32cf5b3aa..c2dd56662 100644 --- a/snovault/root.py +++ b/snovault/root.py @@ -14,6 +14,7 @@ from .appdefs import APP_VERSION_REGISTRY_KEY, ITEM_INDEX_ORDER from .schema_formats import is_accession from .util import SettingsKey +from .project_app import app_project def includeme(config): @@ -124,8 +125,8 @@ class ExtendedHealthPageKey(HealthPageKey): h.BEANSTALK_APP_VERSION: settings.get(s.EB_APP_VERSION), h.BEANSTALK_ENV: env_name, h.BLOB_BUCKET: settings.get(s.BLOB_BUCKET), - h.DATABASE: settings.get(s.SQLALCHEMY_URL).split('@')[1], # don't show user /password - h.DISPLAY_TITLE: "ENCODED Portal Status and Foursight Monitoring", + h.DATABASE: settings.get(s.SQLALCHEMY_URL, 'dummy@postgres').split('@')[1], # don't show user /password + h.DISPLAY_TITLE: f"{app_project().get_app_namespace()} Portal Status and Foursight Monitoring", h.ELASTICSEARCH: settings.get(s.ELASTICSEARCH_SERVER), h.FILE_UPLOAD_BUCKET: settings.get(s.FILE_UPLOAD_BUCKET), h.FOURSIGHT: foursight_url, diff --git a/snovault/tests/root.py b/snovault/tests/root.py index 9c5129cd5..b8d7ea854 100644 --- a/snovault/tests/root.py +++ b/snovault/tests/root.py @@ -8,6 +8,7 @@ Deny, Everyone, ) +from ..root import health_check from ..schema_utils import format_checker from ..calculated import calculated_property from ..resources import Root @@ -19,6 +20,7 @@ def includeme(config): + config.include(health_check) config.scan(__name__) diff --git a/snovault/tests/test_health_path.py b/snovault/tests/test_health_path.py new file mode 100644 index 000000000..0602ae198 --- /dev/null +++ b/snovault/tests/test_health_path.py @@ -0,0 +1,8 @@ +import pytest + + +def test_health_page_basic(testapp): + """ Tests that we can reach the health page and that the customization works """ + health = testapp.get('/health').json + assert health['display_title'] == 'ENCODED Portal Status and Foursight Monitoring' + assert health['database'] == 'postgres' diff --git a/snovault/tests/testappfixtures.py b/snovault/tests/testappfixtures.py index fd6a79cd6..c65569892 100644 --- a/snovault/tests/testappfixtures.py +++ b/snovault/tests/testappfixtures.py @@ -6,6 +6,7 @@ from .. import main # Function main actually defined in __init__.py (should maybe be defined elsewhere) _app_settings = { + 'env.name': 'snovault', 'collection_datastore': 'database', 'item_datastore': 'database', 'load_test_only': True, From 8bb9626c557d7b98471e1988c7320b152ec19e19 Mon Sep 17 00:00:00 2001 From: William Ronchetti Date: Tue, 19 Mar 2024 11:10:36 -0400 Subject: [PATCH 2/6] version --- CHANGELOG.rst | 6 ++++++ pyproject.toml | 2 +- 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index a484e3d43..6dca80e27 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -6,6 +6,12 @@ snovault Change Log ---------- +11.14.0 +======= + +* Allow customization of health page title + + 11.13.0 ======= diff --git a/pyproject.toml b/pyproject.toml index 1b03e0374..d10c5d87b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "dcicsnovault" -version = "11.13.0" +version = "11.14.0" description = "Storage support for 4DN Data Portals." authors = ["4DN-DCIC Team "] license = "MIT" From dbc6c41a84b7def2b2989cf0c73acdef170200da Mon Sep 17 00:00:00 2001 From: William Ronchetti Date: Tue, 19 Mar 2024 11:11:26 -0400 Subject: [PATCH 3/6] pep8 --- snovault/tests/test_health_path.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/snovault/tests/test_health_path.py b/snovault/tests/test_health_path.py index 0602ae198..9a85d82a2 100644 --- a/snovault/tests/test_health_path.py +++ b/snovault/tests/test_health_path.py @@ -1,4 +1,8 @@ import pytest +from dcicutils.misc_utils import ignored + + +ignored(pytest) def test_health_page_basic(testapp): From 7b17db83b24278da5c64b903668f2c30af9bade5 Mon Sep 17 00:00:00 2001 From: William Ronchetti Date: Tue, 19 Mar 2024 15:41:48 -0400 Subject: [PATCH 4/6] repair test on GA --- snovault/root.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/snovault/root.py b/snovault/root.py index c2dd56662..cbfa1e921 100644 --- a/snovault/root.py +++ b/snovault/root.py @@ -112,7 +112,10 @@ class ExtendedHealthPageKey(HealthPageKey): settings = request.registry.settings env_name = settings.get('env.name') - foursight_url = infer_foursight_url_from_env(request=request, envname=env_name) + try: + foursight_url = infer_foursight_url_from_env(request=request, envname=env_name) + except Exception: # this can fail in unit testing depending on env_name + foursight_url = 'Could-not-resolve-foursight' response_dict = { From 1b6cae25e8301c3d19b7a9cd0dd15394215e77a5 Mon Sep 17 00:00:00 2001 From: William Ronchetti Date: Tue, 19 Mar 2024 16:16:36 -0400 Subject: [PATCH 5/6] add env bucket? --- .github/workflows/main.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index e55c0ded1..c38a676c3 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -61,6 +61,7 @@ jobs: if: ${{ matrix.test_type == 'INDEXING' }} env: S3_ENCRYPT_KEY: ${{ secrets.S3_ENCRYPT_KEY }} + GLOBAL_ENV_BUCKET: "foursight-prod-envs" # # The need for this old environment variable name will go away soon. # TRAVIS_JOB_ID: sno-x-test-${{ github.run_number }}- # This will be the new environment variable name. @@ -72,6 +73,7 @@ jobs: if: ${{ matrix.test_type == 'UNIT' }} env: S3_ENCRYPT_KEY: ${{ secrets.S3_ENCRYPT_KEY }} + GLOBAL_ENV_BUCKET: "foursight-prod-envs" # # The need for this old environment variable name will go away soon. # TRAVIS_JOB_ID: sno-x-test-${{ github.run_number }}- # This will be the new environment variable name. @@ -83,6 +85,7 @@ jobs: if: ${{ always() && matrix.test_type == 'INDEXING' }} env: S3_ENCRYPT_KEY: ${{ secrets.S3_ENCRYPT_KEY }} + GLOBAL_ENV_BUCKET: "foursight-prod-envs" # The need for this old environment variable name will go away soon. # TRAVIS_JOB_ID: sno-x-test-${{ github.run_number }}- # This will be the new environment variable name. @@ -94,6 +97,7 @@ jobs: if: ${{ always() && matrix.test_type == 'UNIT' }} env: S3_ENCRYPT_KEY: ${{ secrets.S3_ENCRYPT_KEY }} + GLOBAL_ENV_BUCKET: "foursight-prod-envs" # The need for this old environment variable name will go away soon. # TRAVIS_JOB_ID: sno-x-test-${{ github.run_number }}- # This will be the new environment variable name. From c27f44ff5a3ebf20cfcfe48d708a1db16638461b Mon Sep 17 00:00:00 2001 From: William Ronchetti Date: Thu, 6 Jun 2024 09:35:09 -0400 Subject: [PATCH 6/6] in prog --- snovault/crud_views.py | 20 ++++++++++++++++++++ snovault/loadxl.py | 6 ++++-- snovault/tests/test_post_put_patch.py | 2 +- 3 files changed, 25 insertions(+), 3 deletions(-) diff --git a/snovault/crud_views.py b/snovault/crud_views.py index 819ed83a8..063f9429d 100644 --- a/snovault/crud_views.py +++ b/snovault/crud_views.py @@ -70,6 +70,22 @@ def build_diff_from_request(context, request): return dm.patch_diffs(body) +def build_comparison_from_request(context, request, props): + """ Very similar to above method but runs a comparison instead """ + try: + item_type = context.type_info.name + body = json.loads(request.body) + extract_and_populate_deleted_fields(request, body) + dm = DiffManager(label=item_type) + except json.decoder.JSONDecodeError: + log.info('Request body is not valid JSON!') # can happen from indirect patch, such as with access key + return None + except Exception as e: + log.error('Unknown error encountered building diff from request: %s' % e) + return None + return dm._diffs(props, body) + + def create_item(type_info, request, properties, sheets=None): ''' Validates or generates new UUID, instantiates & saves an Item in @@ -240,6 +256,10 @@ def item_edit(context, request, render=None): render = request.params.get('render', True) # This *sets* the property sheet and adds the item to the indexing queue + check_diff = asbool(request.params.get('check_diff', False)) + if check_diff: + comparison = build_comparison_from_request(context, request, context.properties) + import pdb; pdb.set_trace() update_item(context, request, request.validated) rendered = render_item(request, context, render) diff --git a/snovault/loadxl.py b/snovault/loadxl.py index 7421047e6..9915564a9 100644 --- a/snovault/loadxl.py +++ b/snovault/loadxl.py @@ -684,13 +684,15 @@ def get_schema_info(type_name: str) -> (list, list): if not identifying_path: raise Exception("Item has no uuid nor any other identifying property; cannot PATCH.") normalized_item, deleted_properties = normalize_deleted_properties(an_item) + identifying_path += '?check_diff=true' if deleted_properties: if validate_only and skip_links: - identifying_path += f"?delete_fields={','.join(deleted_properties)}&skip_links=true" + identifying_path += f"&delete_fields={','.join(deleted_properties)}&skip_links=true" else: - identifying_path += f"?delete_fields={','.join(deleted_properties)}" + identifying_path += f"&delete_fields={','.join(deleted_properties)}" elif validate_only and skip_links: identifying_path += f"?skip_links=true" + res = testapp.patch_json(identifying_path, normalized_item) assert res.status_code == 200 patched += 1 diff --git a/snovault/tests/test_post_put_patch.py b/snovault/tests/test_post_put_patch.py index 1e1a758bb..b81eb4163 100644 --- a/snovault/tests/test_post_put_patch.py +++ b/snovault/tests/test_post_put_patch.py @@ -110,7 +110,7 @@ def test_patch(content, testapp): assert res.json['simple1'] == 'simple1 default' assert res.json['simple2'] == 'simple2 default' - res = testapp.patch_json(url, {}, status=200) + res = testapp.patch_json(url+'?check_diff=true', {}, status=200) assert res.json['@graph'][0]['simple1'] == 'simple1 default' assert res.json['@graph'][0]['simple2'] == 'simple2 default'