diff --git a/env.example b/env.example index 176c22c28..9829314bb 100644 --- a/env.example +++ b/env.example @@ -5,9 +5,11 @@ SERVER_DOMAIN=localhost USE_LISTEN_PORT=81 SERVICE_ACCOUNT_CREDS='Provide service account creds' -# Integration testing variables (Optional) +## Opentelemetry configuration variables (Optional) +## Only otlp is supported # TRACING_EXPORT_FORMAT=otlp # LOGGING_EXPORT_FORMAT=otlp -# TRACING_SERVICE_NAME=unique-name-testing -# LOGGING_SERVICE_NAME=unique-name-testing -# LOGGING_INSTANCE_NAME=unique-name-testing \ No newline at end of file +# TRACING_SERVICE_NAME=schematic-api +# LOGGING_SERVICE_NAME=schematic-api +## Other examples: dev, staging, prod +# DEPLOYMENT_ENVIRONMENT=local \ No newline at end of file diff --git a/poetry.lock b/poetry.lock index 0b87e58a1..1f198a588 100644 --- a/poetry.lock +++ b/poetry.lock @@ -35,13 +35,13 @@ dev = ["black", "docutils", "flake8", "ipython", "m2r", "mistune (<2.0.0)", "pyt [[package]] name = "anyio" -version = "4.5.0" +version = "4.6.2.post1" description = "High level compatibility layer for multiple asynchronous event loop implementations" optional = false -python-versions = ">=3.8" +python-versions = ">=3.9" files = [ - {file = "anyio-4.5.0-py3-none-any.whl", hash = "sha256:fdeb095b7cc5a5563175eedd926ec4ae55413bb4be5770c424af0ba46ccb4a78"}, - {file = "anyio-4.5.0.tar.gz", hash = "sha256:c5a275fe5ca0afd788001f58fca1e69e29ce706d746e317d660e21f70c530ef9"}, + {file = "anyio-4.6.2.post1-py3-none-any.whl", hash = "sha256:6d170c36fba3bdd840c73d3868c1e777e33676a69c3a72cf0a0d5d6d8009b61d"}, + {file = "anyio-4.6.2.post1.tar.gz", hash = "sha256:4c8bc31ccdb51c7f7bd251f51c609e038d63e34219b44aa86e47576389880b4c"}, ] [package.dependencies] @@ -52,7 +52,7 @@ typing-extensions = {version = ">=4.1", markers = "python_version < \"3.11\""} [package.extras] doc = ["Sphinx (>=7.4,<8.0)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"] -test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.21.0b1)"] +test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "truststore (>=0.9.1)", "uvloop (>=0.21.0b1)"] trio = ["trio (>=0.26.1)"] [[package]] @@ -449,101 +449,116 @@ files = [ [[package]] name = "charset-normalizer" -version = "3.3.2" +version = "3.4.0" description = "The Real First Universal Charset Detector. 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"sha256:44a72c29cceb0ee08f300b314848c86e57bf8d1f13107a5e671fb9274138d655"}, + {file = "virtualenv-20.27.0.tar.gz", hash = "sha256:2ca56a68ed615b8fe4326d11a0dca5dfbe8fd68510fb6c6349163bed3c15f2b2"}, ] [package.dependencies] @@ -4901,4 +4922,4 @@ aws = ["uWSGI"] [metadata] lock-version = "2.0" python-versions = ">=3.9.0,<3.11" -content-hash = "e72a6816f0534115e5b8cd1c0e55e1e35778e4a059caebfc0b7c2bae96c65a59" +content-hash = "38eaaeb34ea2fe3ba10c11767ba864c4dbab46ff425352256e4ba09ed2369430" diff --git a/pyproject.toml b/pyproject.toml index cccda5718..854c78c13 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -54,7 +54,7 @@ pygsheets = "^2.0.4" PyYAML = "^6.0.0" rdflib = "^6.0.0" setuptools = "^66.0.0" -synapseclient = "4.5.1" +synapseclient = "4.6.0" tenacity = "^8.0.1" toml = "^0.10.2" great-expectations = "^0.15.0" diff --git a/schematic/__init__.py b/schematic/__init__.py index b336be701..8b5e924b1 100644 --- a/schematic/__init__.py +++ b/schematic/__init__.py @@ -3,10 +3,20 @@ import time from typing import Dict, List +import pkg_resources from opentelemetry import trace -from opentelemetry.exporter.otlp.proto.http.trace_exporter import OTLPSpanExporter +from opentelemetry._logs import set_logger_provider +from opentelemetry.exporter.otlp.proto.grpc._log_exporter import OTLPLogExporter +from opentelemetry.exporter.otlp.proto.grpc.trace_exporter import OTLPSpanExporter from opentelemetry.instrumentation.flask import FlaskInstrumentor -from opentelemetry.sdk.resources import SERVICE_NAME, Resource +from opentelemetry.sdk._logs import LoggerProvider, LoggingHandler +from opentelemetry.sdk._logs.export import BatchLogRecordProcessor +from opentelemetry.sdk.resources import ( + DEPLOYMENT_ENVIRONMENT, + SERVICE_NAME, + SERVICE_VERSION, + Resource, +) from opentelemetry.sdk.trace import TracerProvider from opentelemetry.sdk.trace.export import ( BatchSpanProcessor, @@ -48,10 +58,17 @@ def set_up_tracing() -> None: if tracing_export is not None and tracing_export: Synapse.enable_open_telemetry(True) tracing_service_name = os.environ.get("TRACING_SERVICE_NAME", "schematic-api") - + deployment_environment = os.environ.get("DEPLOYMENT_ENVIRONMENT", "") + package_version = pkg_resources.get_distribution("schematicpy").version trace.set_tracer_provider( TracerProvider( - resource=Resource(attributes={SERVICE_NAME: tracing_service_name}) + resource=Resource( + attributes={ + SERVICE_NAME: tracing_service_name, + SERVICE_VERSION: package_version, + DEPLOYMENT_ENVIRONMENT: deployment_environment, + } + ) ) ) FlaskInstrumentor().instrument( @@ -72,6 +89,28 @@ def set_up_tracing() -> None: trace.set_tracer_provider(TracerProvider(sampler=ALWAYS_OFF)) +def set_up_logging() -> None: + """Set up logging to export to OTLP.""" + logging_export = os.environ.get("LOGGING_EXPORT_FORMAT", None) + logging_service_name = os.environ.get("LOGGING_SERVICE_NAME", "schematic-api") + deployment_environment = os.environ.get("DEPLOYMENT_ENVIRONMENT", "") + if logging_export == "otlp": + resource = Resource.create( + { + SERVICE_NAME: logging_service_name, + DEPLOYMENT_ENVIRONMENT: deployment_environment, + } + ) + + logger_provider = LoggerProvider(resource=resource) + set_logger_provider(logger_provider=logger_provider) + + exporter = OTLPLogExporter() + logger_provider.add_log_record_processor(BatchLogRecordProcessor(exporter)) + handler = LoggingHandler(level=logging.NOTSET, logger_provider=logger_provider) + logging.getLogger().addHandler(handler) + + def request_hook(span: Span, environ: Dict) -> None: """ Request hook for the flask server to handle setting attributes in the span. If @@ -112,3 +151,4 @@ def response_hook(span: Span, status: str, response_headers: List) -> None: set_up_tracing() +set_up_logging() diff --git a/schematic/models/validate_attribute.py b/schematic/models/validate_attribute.py index 55a75a5f3..3b148a264 100644 --- a/schematic/models/validate_attribute.py +++ b/schematic/models/validate_attribute.py @@ -11,6 +11,7 @@ import pandas as pd import requests from jsonschema import ValidationError +from opentelemetry import trace from synapseclient import File from synapseclient.core.exceptions import SynapseNoCredentialsError @@ -30,6 +31,7 @@ MessageLevelType = Literal["warning", "error"] ScopeTypes = Literal["set", "value"] +tracer = trace.get_tracer("schematic") class GenerateError: @@ -775,6 +777,7 @@ class ValidateAttribute(object): def __init__(self, dmge: DataModelGraphExplorer) -> None: self.dmge = dmge + @tracer.start_as_current_span("ValidateAttribute::_login") def _login( self, access_token: Optional[str] = None, diff --git a/schematic/store/database/synapse_database_wrapper.py b/schematic/store/database/synapse_database_wrapper.py index 52bf2d4d8..b827b140f 100644 --- a/schematic/store/database/synapse_database_wrapper.py +++ b/schematic/store/database/synapse_database_wrapper.py @@ -5,6 +5,7 @@ import pandas # type: ignore import synapseclient # type: ignore +from opentelemetry import trace from schematic.store.synapse_tracker import SynapseEntityTracker @@ -53,6 +54,9 @@ def __init__( else: syn = synapseclient.Synapse(cache_root_dir=cache_root_dir) syn.login(authToken=auth_token, silent=True) + current_span = trace.get_current_span() + if current_span.is_recording(): + current_span.set_attribute("user.id", syn.credentials.owner_id) self.syn = syn self.synapse_entity_tracker = synapse_entity_tracker or SynapseEntityTracker() diff --git a/schematic/store/synapse.py b/schematic/store/synapse.py index 9993038b5..647fad7ed 100644 --- a/schematic/store/synapse.py +++ b/schematic/store/synapse.py @@ -118,6 +118,15 @@ def _download_manifest_to_folder(self, use_temporary_folder: bool = True) -> Fil download_file=False, retrieve_if_not_present=False, ) + current_span = trace.get_current_span() + if ( + manifest_data + and (file_handle := manifest_data.get("_file_handle", None)) + and current_span.is_recording() + ): + current_span.set_attribute( + "schematic.manifest_size", file_handle.get("contentSize", 0) + ) if manifest_data and manifest_data.path: return manifest_data @@ -309,6 +318,9 @@ def __init__( Consider necessity of adding "columns" and "where_clauses" params to the constructor. Currently with how `query_fileview` is implemented, these params are not needed at this step but could be useful in the future if the need for more scoped querys expands. """ self.syn = self.login(synapse_cache_path, access_token) + current_span = trace.get_current_span() + if current_span.is_recording(): + current_span.set_attribute("user.id", self.syn.credentials.owner_id) self.project_scope = project_scope self.storageFileview = CONFIG.synapse_master_fileview_id self.manifest = CONFIG.synapse_manifest_basename @@ -472,6 +484,9 @@ def login( cache_client=False, ) syn.login(authToken=access_token, silent=True) + current_span = trace.get_current_span() + if current_span.is_recording(): + current_span.set_attribute("user.id", syn.credentials.owner_id) except SynapseHTTPError as exc: raise ValueError( "No access to resources. Please make sure that your token is correct" @@ -486,6 +501,9 @@ def login( cache_client=False, ) syn.login(silent=True) + current_span = trace.get_current_span() + if current_span.is_recording(): + current_span.set_attribute("user.id", syn.credentials.owner_id) return syn def missing_entity_handler(method): @@ -553,6 +571,7 @@ def getPaginatedRestResults(self, currentUserId: str) -> Dict[str, str]: return all_results + @tracer.start_as_current_span("SynapseStorage::getStorageProjects") def getStorageProjects(self, project_scope: List = None) -> list[tuple[str, str]]: """Gets all storage projects the current user has access to, within the scope of the 'storageFileview' attribute. diff --git a/schematic_api/api/routes.py b/schematic_api/api/routes.py index 0cda1f4ac..97484c15c 100644 --- a/schematic_api/api/routes.py +++ b/schematic_api/api/routes.py @@ -560,6 +560,9 @@ def check_entity_type(entity_id): config_handler() syn = SynapseStorage.login(access_token=access_token) + current_span = trace.get_current_span() + if current_span.is_recording(): + current_span.set_attribute("user.id", syn.credentials.owner_id) entity_type = entity_type_mapping(syn=syn, entity_id=entity_id) return entity_type @@ -658,6 +661,9 @@ def download_manifest(manifest_id, new_manifest_name="", as_json=True): # use login method in synapse storage syn = SynapseStorage.login(access_token=access_token) + current_span = trace.get_current_span() + if current_span.is_recording(): + current_span.set_attribute("user.id", syn.credentials.owner_id) try: md = ManifestDownload(syn, manifest_id) manifest_data = md.download_manifest(newManifestName=new_manifest_name) diff --git a/tests/conftest.py b/tests/conftest.py index 3e07bbe86..b1c6ec1fc 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -9,11 +9,6 @@ import pytest from dotenv import load_dotenv from opentelemetry import trace -from opentelemetry._logs import set_logger_provider -from opentelemetry.exporter.otlp.proto.grpc._log_exporter import OTLPLogExporter -from opentelemetry.sdk._logs import LoggerProvider, LoggingHandler -from opentelemetry.sdk._logs.export import BatchLogRecordProcessor -from opentelemetry.sdk.resources import Resource from schematic.configuration.configuration import CONFIG, Configuration from schematic.models.metadata import MetadataModel @@ -227,27 +222,3 @@ def wrap_with_otel(request): """Start a new OTEL Span for each test function.""" with tracer.start_as_current_span(request.node.name): yield - - -@pytest.fixture(scope="session", autouse=True) -def set_up_logging() -> None: - """Set up logging to export to OTLP.""" - logging_export = os.environ.get("LOGGING_EXPORT_FORMAT", None) - logging_service_name = os.environ.get("LOGGING_SERVICE_NAME", "schematic-tests") - logging_instance_name = os.environ.get("LOGGING_INSTANCE_NAME", "local") - if logging_export == "otlp": - resource = Resource.create( - { - "service.name": logging_service_name, - "service.instance.id": logging_instance_name, - } - ) - - logger_provider = LoggerProvider(resource=resource) - set_logger_provider(logger_provider=logger_provider) - - # TODO: Add support for secure connections - exporter = OTLPLogExporter(insecure=True) - logger_provider.add_log_record_processor(BatchLogRecordProcessor(exporter)) - handler = LoggingHandler(level=logging.NOTSET, logger_provider=logger_provider) - logging.getLogger().addHandler(handler)