Source code for thoth.storages.graph.postgres

#!/usr/bin/env python3
# thoth-storages
# Copyright(C) 2019, 2020 Francesco Murdaca, Fridolin Pokorny
#
# This program is free software: you can redistribute it and / or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.

"""An SQL database for storing Thoth data."""

import functools
import re
import logging
import json
import os
import itertools
import weakref
import ssdeep

from decimal import Decimal
from typing import List
from typing import Set
from typing import Tuple
from typing import Optional
from typing import FrozenSet
from typing import Dict
from typing import Union
from typing import Any
from collections import deque
from contextlib import contextmanager
from datetime import datetime

import attr
from packaging.specifiers import SpecifierSet
from packaging.version import parse as parse_version
from sqlalchemy import create_engine
from sqlalchemy import desc
from sqlalchemy import func
from sqlalchemy import exists
from sqlalchemy import and_
from sqlalchemy import tuple_
from sqlalchemy import or_
from sqlalchemy.orm import Query
from sqlalchemy.orm import sessionmaker
from sqlalchemy.orm.session import Session
from sqlalchemy.dialects.postgresql import insert
from sqlalchemy.orm.exc import NoResultFound

from thoth.python import PackageVersion
from thoth.python import Pipfile
from thoth.python import PipfileLock
from thoth.common.helpers import format_datetime
from thoth.common import OpenShift
from thoth.common import normalize_os_version
from thoth.common import map_os_name
from thoth.common.enums import ThothAdviserIntegrationEnum

from .models_base import BaseExtension
from .models import AdviserRun
from .models import ALL_MAIN_MODELS
from .models import CVE
from .models import CVETimestamp
from .models import DebDependency
from .models import DebPackageVersion
from .models import DependencyMonkeyRun
from .models import EcosystemSolver
from .models import ExternalHardwareInformation
from .models import ExternalPythonRequirements
from .models import ExternalPythonRequirementsLock
from .models import ExternalPythonSoftwareStack
from .models import ExternalSoftwareEnvironment
from .models import HardwareInformation
from .models import InspectionRun
from .models import ImportPackage
from .models import KebechetGithubAppInstallations
from .models import PackageExtractRun
from .models import ProvenanceCheckerRun
from .models import PythonArtifact
from .models import PythonFileDigest
from .models import PythonInterpreter
from .models import PythonPackageIndex
from .models import PythonPackageMetadata
from .models import PythonPackageMetadataClassifier
from .models import PythonPackageMetadataDistutils
from .models import PythonPackageMetadataPlatform
from .models import PythonPackageMetadataProjectUrl
from .models import PythonPackageMetadataProvidesExtra
from .models import PythonPackageMetadataRequiresExternal
from .models import PythonPackageMetadataSupportedPlatform
from .models import PythonPackageRequirement
from .models import PythonPackageVersion
from .models import PythonPackageVersionEntity
from .models import PythonPackageVersionEntityRule
from .models import PythonPackageVersionEntityRulesAssociation
from .models import PythonRequirements
from .models import PythonRequirementsLock
from .models import PythonSoftwareStack
from .models import RPMPackageVersion
from .models import RPMRequirement
from .models import SecurityIndicatorAggregatedRun
from .models import SoftwareEnvironment
from .models import VersionedSymbol

from .models import Advised
from .models import DebDepends
from .models import DebPreDepends
from .models import DebReplaces
from .models import DependsOn
from .models import DetectedSymbol
from .models import FoundDeb
from .models import FoundImportPackage
from .models import FoundPythonFile
from .models import FoundPythonInterpreter
from .models import FoundRPM
from .models import HasArtifact
from .models import HasExternalPythonRequirements
from .models import HasExternalPythonRequirementsLock
from .models import HasPythonRequirements
from .models import HasPythonRequirementsLock
from .models import HasMetadataClassifier
from .models import HasMetadataDistutils
from .models import HasMetadataPlatform
from .models import HasMetadataProjectUrl
from .models import HasMetadataProvidesExtra
from .models import HasMetadataRequiresExternal
from .models import HasMetadataSupportedPlatform
from .models import HasSymbol
from .models import HasUnresolved
from .models import HasVulnerability
from .models import Identified
from .models import PythonDependencyMonkeyRequirements
from .models import RequiresSymbol
from .models import RPMRequires
from .models import SIAggregated
from .models import Solved
from .models import ALL_RELATION_MODELS

from .models_performance import PERFORMANCE_MODEL_BY_NAME, ALL_PERFORMANCE_MODELS
from .models_performance import PERFORMANCE_MODELS_ML_FRAMEWORKS

from .sql_base import SQLBase
from .models_base import Base
from .postgres_utils import database_exists
from .postgres_utils import create_database
from .query_result_base import PythonQueryResult
from .enums import EnvironmentTypeEnum
from .enums import SoftwareStackTypeEnum
from .enums import InspectionSyncStateEnum
from .enums import MetadataDistutilsTypeEnum
from .enums import QuerySortTypeEnum
from .enums import PlatformEnum
from .enums import KebechetManagerEnum

from ..analyses import AnalysisResultsStore
from ..dependency_monkey_reports import DependencyMonkeyReportsStore
from ..provenance import ProvenanceResultsStore
from ..solvers import SolverResultsStore
from ..advisers import AdvisersResultsStore
from ..exceptions import NotFoundError
from ..exceptions import PythonIndexNotRegistered
from ..exceptions import PerformanceIndicatorNotRegistered
from ..exceptions import PythonIndexNotProvided
from ..exceptions import SolverNotRun
from ..exceptions import NotConnected
from ..exceptions import AlreadyConnected
from ..exceptions import DatabaseNotInitialized
from ..exceptions import DistutilsKeyNotKnown
from ..exceptions import SortTypeQueryError
from ..exceptions import CudaVersionDoesNotMatch


# Name of environment variables are long
# intentionally - you should adjust them only if
# you know what do you do.
_HAS_PYTHON_SOLVER_ERROR_CACHE_SIZE = int(os.getenv("THOTH_STORAGE_HAS_PYTHON_SOLVER_ERROR_CACHE_SIZE", 4096))
_GET_PYTHON_PACKAGE_VERSION_RECORDS_CACHE_SIZE = int(
    os.getenv("THOTH_STORAGE_GET_PYTHON_PACKAGE_VERSION_RECORDS_CACHE_SIZE", 16384)
)
_GET_DEPENDS_ON_CACHE_SIZE = int(os.getenv("THOTH_STORAGE_GET_DEPENDS_ON_CACHE_SIZE", 8192))
_GET_PYTHON_CVE_RECORDS_ALL_CACHE_SIZE = int(os.getenv("THOTH_STORAGE_GET_PYTHON_CVE_RECORDS_ALL_CACHE_SIZE", 4096))
_GET_PYTHON_PACKAGE_REQUIRED_SYMBOLS_CACHE_SIZE = int(
    os.getenv("THOTH_STORAGE_GET_PYTHON_PACKAGE_REQUIRED_SYMBOLS_CACHE_SIZE", 4096)
)
_GET_PYTHON_ENVIRONMENT_MARKER_CACHE_SIZE = int(os.getenv("THOTH_GET_PYTHON_ENVIRONMENT_MARKER_CACHE_SIZE", 4096))
_GET_S2I_ANALYZED_IMAGE_SYMBOLS = int(os.getenv("THOTH_S2I_ANALYZED_IMAGE_SYMBOLS_CACHE_SIZE", 1))
_GET_SI_AGGREGATED_PYTHON_PACKAGE_VERSION_CACHE_SIZE = int(
    os.getenv("THOTH_GET_PYTHON_ENVIRONMENT_MARKER_CACHE_SIZE", 4096)
)
_GET_PYTHON_PYTHON_PACKAGE_VERSION_SOLVER_RULES_CACHE_SIZE = int(
    os.getenv("THOTH_GET_PYTHON_PYTHON_PACKAGE_VERSION_SOLVER_RULES_CACHE_SIZE", 4096)
)
_GET_RPM_PACKAGE_VERSION_CACHE_SIZE = int(os.getenv("THOTH_GET_RPM_PACKAGE_VERSION_CACHE_SIZE", 1))
_GET_PYTHON_PACKAGE_VERSION_CACHE_SIZE = int(os.getenv("THOTH_GET_PYTHON_PACKAGE_VERSION_CACHE_SIZE", 1))


_LOGGER = logging.getLogger(__name__)


[docs]def lru_cache(*lru_args, **lru_kwargs): """Implement a cache for methods. Based on: https://stackoverflow.com/questions/33672412/python-functools-lru-cache-with-class-methods-release-object """ # XXX: possibly move to another module to make it available for the whole Thoth def decorator(func): @functools.wraps(func) def wrapped_func(self, *args, **kwargs): # We're storing the wrapped method inside the instance. If we had # a strong reference to self the instance would never die. self_weak = weakref.ref(self) @functools.wraps(func) @functools.lru_cache(*lru_args, **lru_kwargs) def cached_method(*args, **kwargs): return func(self_weak(), *args, **kwargs) setattr(self, func.__name__, cached_method) self._CACHED_METHODS.append(cached_method) return cached_method(*args, **kwargs) return wrapped_func return decorator
[docs]@attr.s() class GraphDatabase(SQLBase): """A SQL database adapter providing graph-like operations on top of SQL queries.""" _DECLARATIVE_BASE = Base DEFAULT_COUNT = 100 _MULTI_VALUE_KEY_PYTHON_PACKAGE_METADATA_MAP = { "classifier": [HasMetadataClassifier, PythonPackageMetadataClassifier, "classifier"], "platform": [HasMetadataPlatform, PythonPackageMetadataPlatform, "platform"], "supported_platform": [ HasMetadataSupportedPlatform, PythonPackageMetadataSupportedPlatform, "supported_platform", ], "requires_external": [HasMetadataRequiresExternal, PythonPackageMetadataRequiresExternal, "requires_external"], "project_url": [HasMetadataProjectUrl, PythonPackageMetadataProjectUrl, "project_url"], "provides_extra": [HasMetadataProvidesExtra, PythonPackageMetadataProvidesExtra, "optional_feature"], } _CACHED_METHODS = [] def __del__(self) -> None: """Destruct adapter object.""" if int(bool(os.getenv("THOTH_STORAGES_LOG_STATS", 0))): stats = self.stats() _LOGGER.info("Graph adapter statistics:\n%s", json.dumps(stats, indent=2))
[docs] @staticmethod def construct_connection_string() -> str: """Construct a connection string needed to connect to database.""" connection_string = ( f"postgresql+psycopg2://" f"{os.getenv('KNOWLEDGE_GRAPH_USER', 'postgres')}:{os.getenv('KNOWLEDGE_GRAPH_PASSWORD', 'postgres')}" f"@{os.getenv('KNOWLEDGE_GRAPH_HOST', 'localhost')}:{os.getenv('KNOWLEDGE_GRAPH_PORT', 5432)}" f"/{os.getenv('KNOWLEDGE_GRAPH_DATABASE', 'postgres')}" ) if bool(int(os.getenv("KNOWLEDGE_GRAPH_SSL_DISABLED", 0))): connection_string += "?sslmode=disable" return connection_string
@contextmanager def _session_scope(self) -> Session: """Handle session commit and rollback.""" session = self._sessionmaker() try: yield session session.commit() except Exception: session.rollback() raise finally: session.close()
[docs] def connect(self): """Connect to the database.""" if self.is_connected(): raise AlreadyConnected("Cannot connect, the adapter is already connected") echo = bool(int(os.getenv("THOTH_STORAGES_DEBUG_QUERIES", 0))) try: self._engine = create_engine(self.construct_connection_string(), echo=echo) self._sessionmaker = sessionmaker(bind=self._engine) except Exception as engine_exc: _LOGGER.warning("Failed to create engine: %s", str(engine_exc)) # Drop engine and session in case of any connection issues so is_connected behaves correctly. if self._engine: try: self._engine.dispose() except Exception as exc: _LOGGER.warning("Failed to dispose engine: %s", str(exc)) pass self._engine = None self._sessionmaker = None raise if not database_exists(self._engine.url): _LOGGER.warning("The database has not been created yet, no check for schema version is performed") return try: if not self.is_schema_up2date(): _LOGGER.debug("Database adapter connected, database is initialized") except DatabaseNotInitialized as exc: _LOGGER.warning("Database is not ready to receive or query data: %s", str(exc))
@staticmethod def _get_alembic_configuration(): import thoth.storages from alembic import config alembic_cfg = config.Config(os.path.join(os.path.dirname(thoth.storages.__file__), "data", "alembic.ini")) alembic_cfg.attributes["configure_logger"] = False alembic_cfg.set_section_option( "alembic", "script_location", os.path.join(os.path.dirname(thoth.storages.__file__), "data", "alembic") ) return alembic_cfg
[docs] def initialize_schema(self): """Initialize schema of database.""" from alembic import command if not self.is_connected(): raise NotConnected("Cannot initialize schema: the adapter is not connected yet") if not database_exists(self._engine.url): _LOGGER.info("The database has not been created yet, it will be created now...") create_database(self._engine.url) alembic_cfg = self._get_alembic_configuration() # Overwrite URL based on deployment configuration. alembic_cfg.set_main_option("sqlalchemy.url", self.construct_connection_string()) command.upgrade(alembic_cfg, "head")
[docs] def drop_all(self): """Drop all content stored in the database.""" super().drop_all() # Drop alembic version to be able re-run alembic migrations next time. self._engine.execute("DROP TABLE alembic_version;")
def _get_script_directory_revisions(self): from alembic import script alembic_cfg = self._get_alembic_configuration() directory = script.ScriptDirectory.from_config(alembic_cfg) return directory
[docs] def get_script_alembic_version_head(self) -> str: """Get alembic version head from alembic folder scripts.""" directory = self._get_script_directory_revisions() head_revision = directory.get_current_head() return head_revision
[docs] def get_table_alembic_version_head(self) -> str: """Get alembic version head from database table.""" query = f"SELECT * FROM alembic_version" with self._session_scope() as session: result = session.execute(query).fetchone() return result[0]
[docs] def is_schema_up2date(self) -> bool: """Check if the current schema is up2date with the one configured on database side.""" database_head = self.get_table_alembic_version_head() script_head = self.get_script_alembic_version_head() is_up2date = database_head == script_head if not is_up2date: _LOGGER.warning( "The database schema is not in sync with library head revision, the current library revision " "head: %r, database head: %r", script_head, database_head, ) return is_up2date
[docs] def get_alembic_version_count_all(self) -> int: """Get number of records in alembic version table (1 expected).""" query = f"SELECT COUNT(*) FROM alembic_version" with self._session_scope() as session: result = session.execute(query).fetchone() return result[0]
[docs] @staticmethod def normalize_python_package_name(package_name: str) -> str: """Normalize Python package name based on PEP-0503.""" return PackageVersion.normalize_python_package_name(package_name)
[docs] @staticmethod def normalize_python_package_version(package_version: str) -> str: """Normalize Python package name based on PEP-440.""" return PackageVersion.normalize_python_package_version(package_version)
[docs] @staticmethod def normalize_python_index_url(index_url: Optional[str]) -> Optional[str]: """Map python index url.""" if index_url == "https://pypi.python.org/simple": return "https://pypi.org/simple" return index_url
[docs] def get_analysis_metadata(self, analysis_document_id: str) -> Dict[str, Any]: """Get metadata stored for the given analysis document. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_analysis_metadata() { 'analysis_datetime': datetime(2019, 10, 7, 18, 57, 22, 658131), 'analysis_document_id': 'package-extract-2ef02c9cea8b1ef7', 'package_extract_name': 'thoth-package-extract', 'package_extract_version': '1.0.1' } """ with self._session_scope() as session: query = ( session.query(PackageExtractRun) .filter(PackageExtractRun.analysis_document_id == analysis_document_id) .with_entities( PackageExtractRun.datetime, PackageExtractRun.analysis_document_id, PackageExtractRun.package_extract_name, PackageExtractRun.package_extract_version, ) ) query_result = query.first() if query_result is None: raise NotFoundError(f"No records found for analysis with id {analysis_document_id!r}") return { "analysis_datetime": query_result[0], "analysis_document_id": query_result[1], "package_extract_name": query_result[2], "package_extract_version": query_result[3], }
def _do_software_environment_listing( self, start_offset: int, count: Optional[int], is_external: bool, environment_type: str ) -> List[str]: """Perform actual query to software environments.""" if is_external: class_ = ExternalSoftwareEnvironment else: class_ = SoftwareEnvironment with self._session_scope() as session: result = ( session.query(class_.environment_name) .filter(class_.environment_type == environment_type) .offset(start_offset) .limit(count) .all() ) return [item[0] for item in result]
[docs] def get_run_software_environment_all( self, start_offset: int = 0, count: Optional[int] = DEFAULT_COUNT, is_external: bool = False ) -> List[str]: """Get all software environments available for run. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_run_software_environment_all() ['quay.io/thoth-station/thoth-pylint:v0.7.0-ubi8'] """ return self._do_software_environment_listing( start_offset, count, is_external, EnvironmentTypeEnum.RUNTIME.value )
[docs] def get_build_software_environment_all( self, start_offset: int = 0, count: Optional[int] = DEFAULT_COUNT ) -> List[str]: """Get all software environments available for build. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_run_software_environment_all() ['quay.io/thoth-station/thoth-pylint:v0.7.0-ubi8'] """ # We do not have external/user software environment which is build environment yet. return self._do_software_environment_listing(start_offset, count, False, EnvironmentTypeEnum.BUILDTIME.value)
def _do_software_environment_analyses_listing( self, software_environment_name: str, start_offset: int, count: Optional[int], convert_datetime: bool, is_external: bool, environment_type: str, ) -> List[dict]: """Get listing of available software environment analyses.""" if is_external: class_ = ExternalSoftwareEnvironment else: class_ = SoftwareEnvironment with self._session_scope() as session: query_result = ( session.query(class_) .filter(class_.environment_type == environment_type) .filter(class_.environment_name == software_environment_name) .join(PackageExtractRun) .with_entities( PackageExtractRun.datetime, PackageExtractRun.analysis_document_id, PackageExtractRun.package_extract_name, PackageExtractRun.package_extract_version, ) .offset(start_offset) .limit(count) .all() ) result = [] for item in query_result: result.append( { "analysis_datetime": item[0] if not convert_datetime else format_datetime(item[0]), "analysis_document_id": item[1], "package_extract_name": item[2], "package_extract_version": item[3], } ) return result
[docs] def get_run_software_environment_analyses_all( self, run_software_environment_name: str, start_offset: int = 0, count: Optional[int] = DEFAULT_COUNT, convert_datetime: bool = True, is_external: bool = False, ) -> List[dict]: """Get listing of analyses available for the given software environment for run. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_run_software_environment_analyses_all() [{ 'analysis_datetime': datetime(2019, 10, 7, 18, 57, 22, 658131), 'analysis_document_id': 'package-extract-2ef02c9cea8b1ef7', 'package_extract_name': 'thoth-package-extract', 'package_extract_version': '1.0.1' }] """ return self._do_software_environment_analyses_listing( run_software_environment_name, start_offset=start_offset, count=count, is_external=is_external, convert_datetime=convert_datetime, environment_type=EnvironmentTypeEnum.RUNTIME.value, )
[docs] def get_build_software_environment_analyses_all( self, build_software_environment_name: str, start_offset: int = 0, count: Optional[int] = DEFAULT_COUNT, convert_datetime: bool = True, is_external: bool = False, ) -> List[dict]: """Get listing of analyses available for the given software environment for build.""" return self._do_software_environment_analyses_listing( build_software_environment_name, start_offset=start_offset, count=count, is_external=is_external, convert_datetime=convert_datetime, environment_type=EnvironmentTypeEnum.BUILDTIME.value, )
[docs] def python_package_version_exists( self, package_name: str, package_version: str, index_url: Optional[str] = None, solver_name: Optional[str] = None, ) -> bool: """Check if the given Python package version exists in the graph database. If optional solver_name parameter is set, the call answers if the given package was solved by the given solver. Otherwise, any solver run is taken into account. """ package_name = self.normalize_python_package_name(package_name) package_version = self.normalize_python_package_version(package_version) index_url = self.normalize_python_index_url(index_url) with self._session_scope() as session: query = ( session.query(PythonPackageVersion) .filter(PythonPackageVersion.package_name == package_name) .filter(PythonPackageVersion.package_version == package_version) ) if solver_name: solver_info = OpenShift.parse_python_solver_name(solver_name) os_name = map_os_name(solver_info["os_name"]) os_version = solver_info["os_version"] python_version = solver_info["python_version"] query = ( query.filter(PythonPackageVersion.os_name == os_name) .filter(PythonPackageVersion.os_version == os_version) .filter(PythonPackageVersion.python_version == python_version) ) if index_url: query = query.join(PythonPackageIndex).filter(PythonPackageIndex.url == index_url) return query.count() > 0
[docs] def python_package_exists(self, package_name: str) -> bool: """Check if the given Python package exists regardless of version.""" package_name = self.normalize_python_package_name(package_name) with self._session_scope() as session: return ( session.query(PythonPackageVersionEntity) .filter(PythonPackageVersion.package_name == package_name) .count() > 0 )
[docs] def solved_software_environment_exists(self, os_name: str, os_version: str, python_version: str) -> bool: """Check if there are any solved packages for the given software environment.""" os_name = map_os_name(os_name) os_version = normalize_os_version(os_name, os_version) with self._session_scope() as session: result = session.query( session.query(PythonPackageVersion) .filter( PythonPackageVersion.os_name == os_name, PythonPackageVersion.os_version == os_version, PythonPackageVersion.python_version == python_version, ) .exists() ).scalar() return result
[docs] def get_solved_python_package_versions_software_environment_all(self) -> List[Dict[str, str]]: """Retrieve software environment configurations used to solve Python packages.""" with self._session_scope() as session: result = ( session.query(EcosystemSolver) .with_entities(EcosystemSolver.os_name, EcosystemSolver.os_version, EcosystemSolver.python_version) .distinct() .all() ) return [{"os_name": i[0], "os_version": i[1], "python_version": i[2]} for i in result]
[docs] @lru_cache(maxsize=_HAS_PYTHON_SOLVER_ERROR_CACHE_SIZE) def has_python_solver_error( self, package_name: str, package_version: str, index_url: str, *, os_name: Union[str, None], os_version: Union[str, None], python_version: Union[str, None], ) -> bool: """Retrieve information whether the given package has any solver error.""" package_name = self.normalize_python_package_name(package_name) package_version = self.normalize_python_package_version(package_version) os_name = map_os_name(os_name) os_version = normalize_os_version(os_name, os_version) index_url = self.normalize_python_index_url(index_url) with self._session_scope() as session: query = ( session.query(PythonPackageVersion) .filter(PythonPackageVersion.package_name == package_name) .filter(PythonPackageVersion.package_version == package_version) ) if os_name is not None: query = query.filter(PythonPackageVersion.os_name == os_name) if os_version is not None: query = query.filter(PythonPackageVersion.os_version == os_version) if python_version is not None: query = query.filter(PythonPackageVersion.python_version == python_version) query = ( query.join(PythonPackageIndex) .filter(PythonPackageIndex.url == index_url) .join(Solved) .order_by(desc(Solved.datetime)) .with_entities(Solved.error) ) result = query.first() if result is None: raise NotFoundError( f"No package record found for {package_name!r} in version {package_version!r} " f"from {index_url!r}, OS name is {os_name!r}:{os_version!r} with Python version {python_version!r}" ) return result[0]
@staticmethod def _count_per_package(result: Union[List, Dict[str, Any]]) -> Dict[Tuple[str, str, str], int]: """Format Query result to count per package.""" query_result = {} for item in result: if (item[0], item[1], item[2]) not in query_result: query_result[(item[0], item[1], item[2])] = item[3] else: query_result[(item[0], item[1], item[2])] += item[3] return query_result @staticmethod def _count_per_index(result: Union[List, Dict[str, Any]], index_url: str) -> Dict[str, Dict[Tuple[str, str], int]]: """Format Query result to count per index.""" index_url = GraphDatabase.normalize_python_index_url(index_url) query_result = {index_url: {}} for item in result: if item[2] == index_url: if (item[0], item[1]) not in query_result[index_url].keys(): query_result[index_url][(item[0], item[1])] = item[3] else: query_result[index_url][(item[0], item[1])] += item[3] return query_result @staticmethod def _count_per_version( result: Union[List, Dict[str, Any]], ) -> Dict[str, Dict[str, int]]: """Format Query result to count per version.""" query_result = {} for item in result: if item[1] not in query_result: query_result[item[1]] = {} query_result[item[1]][item[2]] = item[3] else: if item[2] not in query_result[item[1]]: query_result[item[1]][item[2]] = item[3] else: query_result[item[1]][item[2]] += item[3] return query_result @staticmethod def _group_by_package_name( result: Union[List, Dict[str, Any]], ) -> Dict[str, List[Tuple[str, str]]]: """Format Query result to group by package name.""" query_result = {} for item in result: if item[0] not in query_result: query_result[item[0]] = [] query_result[item[0]].append((item[1], item[2])) return query_result # Solved Python Packages
[docs] def get_solved_python_packages_all( self, *, start_offset: int = 0, count: Optional[int] = DEFAULT_COUNT, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, distinct: bool = False, ) -> List[Tuple[str, str]]: """Retrieve solved Python package with index in Thoth Database. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_solved_python_packages_all() [('regex', 'https://pypi.org/simple'), ('tensorflow', 'https://pypi.org/simple')] """ os_name = map_os_name(os_name) os_version = normalize_os_version(os_name, os_version) return self.__class__.get_python_packages_all(**locals())
def _construct_solved_python_packages_query( self, session: Session, *, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, ) -> Query: """Construct query for solved Python packages functions, the query is not executed.""" kwargs = locals() kwargs.pop("self", None) # static method return self.__class__._construct_python_packages_query(**kwargs)
[docs] def get_solved_python_packages_count_all( self, *, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, distinct: bool = False, ) -> int: """Retrieve number of solved Python package versions in Thoth Database.""" os_name = map_os_name(os_name) os_version = normalize_os_version(os_name, os_version) with self._session_scope() as session: query = self._construct_solved_python_packages_query( session, os_name=os_name, os_version=os_version, python_version=python_version ) if distinct: query = query.distinct() return query.count()
[docs] def get_solved_python_packages_all_versions( self, *, start_offset: int = 0, count: Optional[int] = DEFAULT_COUNT, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, distinct: bool = False, ) -> Dict[str, List[Tuple[str, str]]]: """Retrieve solved Python package versions per package in Thoth Database. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_solved_python_packages_all_versions() {'absl-py': [('0.1.10', 'https://pypi.org/simple'), ('0.2.1', 'https://pypi.org/simple')]} """ os_name = map_os_name(os_name) os_version = normalize_os_version(os_name, os_version) with self._session_scope() as session: query = self._construct_solved_python_packages_query( session, os_name=os_name, os_version=os_version, python_version=python_version ) query = query.offset(start_offset).limit(count) if distinct: query = query.distinct() result = query.all() query_result = {} for item in result: if item[0] not in query_result: query_result[item[0]] = [] query_result[item[0]].append((item[1], item[2])) return query_result
[docs] def get_solved_python_package_versions_count( self, *, start_offset: int = 0, count: Optional[int] = DEFAULT_COUNT, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, distinct: bool = False, ) -> Dict[Tuple[str, str, str], int]: """Retrieve number of Python Package (package_name, package_version, index_url) solved in Thoth Database. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_solved_python_package_versions_count() {('absl-py', '0.1.10', 'https://pypi.org/simple'): 1, ('absl-py', '0.2.1', 'https://pypi.org/simple'): 1} """ os_name = map_os_name(os_name) os_version = normalize_os_version(os_name, os_version) return self.__class__.get_python_package_versions_count(**locals())
[docs] def get_solved_python_package_versions_count_per_index( self, index_url: str, *, start_offset: int = 0, count: Optional[int] = DEFAULT_COUNT, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, distinct: bool = False, ) -> Dict[str, Dict[Tuple[str, str], int]]: """Retrieve number of solved Python package versions per index url in Thoth Database. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_solved_python_package_versions_count_per_index(index_url='https://pypi.org/simple') {'https://pypi.org/simple': {('absl-py', '0.1.10'): 1, ('absl-py', '0.2.1'): 1}} """ os_name = map_os_name(os_name) os_version = normalize_os_version(os_name, os_version) index_url = self.normalize_python_index_url(index_url) return self.__class__.get_python_package_versions_count_per_index(**locals())
[docs] def get_solved_python_package_versions_count_per_version( self, package_name: str, *, start_offset: int = 0, count: Optional[int] = DEFAULT_COUNT, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, distinct: bool = False, ) -> Dict[str, Dict[str, int]]: """Retrieve number of solved Python package versions per package version in Thoth Database. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_solved_python_package_versions_count_per_version(package_name='tensorflow') {'1.14.0rc0': {'https://pypi.org/simple': 1}, '1.13.0rc2': {'https://pypi.org/simple': 1}} """ os_name = map_os_name(os_name) os_version = normalize_os_version(os_name, os_version) return self.__class__.get_python_package_versions_count_per_version(**locals())
def _construct_solved_python_package_versions_query( self, session: Session, package_name: Optional[str] = None, package_version: Optional[str] = None, index_url: Optional[str] = None, *, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, is_missing: Optional[bool] = None, ) -> Query: """Construct query for solved Python packages versions functions, the query is not executed.""" index_url = self.normalize_python_index_url(index_url) return self.__class__._construct_python_package_versions_query(**locals())
[docs] def get_solved_python_package_versions_all( self, package_name: Optional[str] = None, package_version: Optional[str] = None, index_url: Optional[str] = None, *, start_offset: int = 0, count: Optional[int] = DEFAULT_COUNT, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, distinct: bool = False, is_missing: Optional[bool] = None, ) -> List[Tuple[str, str, str]]: """Retrieve solved Python package versions in Thoth Database. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_solved_python_package_versions_all() [('regex', '2018.11.7', 'https://pypi.org/simple'), ('tensorflow', '1.11.0', 'https://pypi.org/simple')] """ os_name = map_os_name(os_name) os_version = normalize_os_version(os_name, os_version) with self._session_scope() as session: query = self._construct_solved_python_package_versions_query( session, package_name=package_name, package_version=package_version, index_url=index_url, os_name=os_name, os_version=os_version, python_version=python_version, is_missing=is_missing, ) query = query.offset(start_offset).limit(count) if distinct: query = query.distinct() return query.all()
[docs] def get_solved_python_package_versions_count_all( self, package_name: Optional[str] = None, package_version: Optional[str] = None, index_url: Optional[str] = None, *, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, distinct: bool = False, is_missing: Optional[bool] = None, ) -> int: """Retrieve solved Python package versions number in Thoth Database.""" os_name = map_os_name(os_name) os_version = normalize_os_version(os_name, os_version) index_url = self.normalize_python_index_url(index_url) with self._session_scope() as session: query = self._construct_solved_python_package_versions_query( session, package_name=package_name, package_version=package_version, index_url=index_url, os_name=os_name, os_version=os_version, python_version=python_version, is_missing=is_missing, ) if distinct: query = query.distinct() return query.count()
def _construct_error_solved_python_package_versions_query( self, session: Session, package_name: Optional[str] = None, package_version: Optional[str] = None, index_url: Optional[str] = None, *, unsolvable: bool = False, unparseable: bool = False, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, ) -> Query: """Construct query for solved with error Python packages versions functions, the query is not executed.""" query = session.query(PythonPackageVersion) if package_name is not None: package_name = self.normalize_python_package_name(package_name) query = query.filter(PythonPackageVersion.package_name == package_name) if package_version is not None: package_version = self.normalize_python_package_version(package_version) query = query.filter(PythonPackageVersion.package_version == package_version) if index_url is not None: index_url = self.normalize_python_index_url(index_url) query = query.filter(PythonPackageIndex.url == index_url) conditions = [Solved.version_id == PythonPackageVersion.id, Solved.error.is_(True)] if unsolvable: conditions.append(Solved.error_unsolvable.is_(True)) if unparseable: conditions.append(Solved.error_unparseable.is_(True)) if os_name: os_name = map_os_name(os_name) conditions.append(PythonPackageVersion.os_name == os_name) if os_version: os_version = normalize_os_version(os_name, os_version) conditions.append(PythonPackageVersion.os_version == os_version) if python_version: conditions.append(PythonPackageVersion.python_version == python_version) query = query.filter(exists().where(and_(*conditions))) return query
[docs] def get_error_solved_python_package_versions_all( self, package_name: Optional[str] = None, package_version: Optional[str] = None, index_url: Optional[str] = None, *, unsolvable: bool = False, unparseable: bool = False, start_offset: int = 0, count: Optional[int] = DEFAULT_COUNT, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, distinct: bool = False, ) -> List[Tuple[str, str, str]]: """Retrieve solved with error Python package versions in Thoth Database. if unsolvable=True -> get_unsolvable_python_package_versions if unparseable=True -> get_unparseable_python_package_versions Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_error_solved_python_package_versions_all() [('regex', '2018.11.7', 'https://pypi.org/simple'), ('tensorflow', '1.11.0', 'https://pypi.org/simple')] """ os_name = map_os_name(os_name) os_version = normalize_os_version(os_name, os_version) index_url = self.normalize_python_index_url(index_url) if unsolvable is True and unparseable is True: raise ValueError("Cannot query for unparseable and unsolvable at the same time") with self._session_scope() as session: query = self._construct_error_solved_python_package_versions_query( session, package_name=package_name, package_version=package_version, index_url=index_url, unsolvable=unsolvable, unparseable=unparseable, os_name=os_name, os_version=os_version, python_version=python_version, ) query = query.join(PythonPackageIndex).with_entities( PythonPackageVersion.package_name, PythonPackageVersion.package_version, PythonPackageIndex.url ) query = query.offset(start_offset).limit(count) if distinct: query = query.distinct() return query.all()
[docs] def get_error_solved_document_id_all( self, package_name: Optional[str] = None, package_version: Optional[str] = None, index_url: Optional[str] = None, *, unsolvable: bool = False, unparseable: bool = False, start_offset: int = 0, count: Optional[int] = DEFAULT_COUNT, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, distinct: bool = False, limit_results: bool = True, ) -> List[str]: """Retrieve solver document id with error Python package versions in Thoth Database. if unsolvable=True -> get_unsolvable_python_package_versions if unparseable=True -> get_unparseable_python_package_versions Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_error_solved_document_id_all() ['solver-fedora-32-py37-324232'] """ if unsolvable is True and unparseable is True: raise ValueError("Cannot query for unparseable and unsolvable at the same time") os_name = map_os_name(os_name) os_version = normalize_os_version(os_name, os_version) with self._session_scope() as session: query = self._construct_error_solved_python_package_versions_query( session, package_name=package_name, package_version=package_version, index_url=index_url, unsolvable=unsolvable, unparseable=unparseable, os_name=os_name, os_version=os_version, python_version=python_version, ) query = query.with_entities(Solved.document_id) if limit_results: query = query.offset(start_offset).limit(count) if distinct: query = query.distinct() return [ids[0] for ids in query.all()]
[docs] def get_error_solved_python_package_versions_count_all( self, package_name: Optional[str] = None, package_version: Optional[str] = None, index_url: Optional[str] = None, *, unsolvable: bool = False, unparseable: bool = False, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, distinct: bool = False, ) -> int: """Retrieve solved with error Python package versions number in Thoth Database. if unsolvable=True -> get_unsolvable_python_package_versions_count_all if unparseable=True -> get_unparseable_python_package_versions_count_all """ os_name = map_os_name(os_name) os_version = normalize_os_version(os_name, os_version) index_url = self.normalize_python_index_url(index_url) if unsolvable is True and unparseable is True: raise ValueError("Cannot query for unparseable and unsolvable at the same time") with self._session_scope() as session: query = self._construct_error_solved_python_package_versions_query( session, package_name=package_name, package_version=package_version, index_url=index_url, unsolvable=unsolvable, unparseable=unparseable, os_name=os_name, os_version=os_version, python_version=python_version, ) query = query.join(PythonPackageIndex).with_entities( PythonPackageVersion.package_name, PythonPackageVersion.package_version, PythonPackageIndex.url ) if distinct: query = query.distinct() return query.count()
# Unsolved Python Packages def _construct_unsolved_python_package_versions_query( self, session: Session, package_name: Optional[str] = None, package_version: Optional[str] = None, index_url: Optional[str] = None, *, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, ) -> Query: """Construct query for unsolved Python packages versions functions, the query is not executed.""" index_url = self.normalize_python_index_url(index_url) query = session.query(PythonPackageVersionEntity).filter( PythonPackageVersionEntity.package_version.isnot(None), PythonPackageIndex.url.isnot(None), PythonPackageIndex.enabled.is_(True), ) query = query.join(PythonPackageVersionEntityRulesAssociation, isouter=True).filter( PythonPackageVersionEntityRulesAssociation.python_package_version_entity_id.is_(None) ) if package_name is not None: package_name = self.normalize_python_package_name(package_name) query = query.filter(PythonPackageVersionEntity.package_name == package_name) if package_version is not None: package_version = self.normalize_python_package_version(package_version) query = query.filter(PythonPackageVersionEntity.package_version == package_version) if index_url is not None: index_url = self.normalize_python_index_url(index_url) query = query.filter(PythonPackageIndex.url == index_url) conditions = [PythonPackageVersionEntity.id == PythonPackageVersion.entity_id] if os_name: conditions.append(PythonPackageVersion.os_name == os_name) if os_version: conditions.append(PythonPackageVersion.os_version == os_version) if python_version: conditions.append(PythonPackageVersion.python_version == python_version) return query.filter(~exists().where(and_(*conditions)))
[docs] def get_unsolved_python_packages_all( self, *, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, start_offset: int = 0, count: Optional[int] = DEFAULT_COUNT, distinct: bool = False, ) -> List[Tuple[str, Optional[str]]]: """Retrieve unsolved Python package with index in Thoth Database. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_unsolved_python_packages_all() [('regex', 'https://pypi.org/simple'), ('tensorflow', 'https://pypi.org/simple')] """ os_name = map_os_name(os_name) os_version = normalize_os_version(os_name, os_version) with self._session_scope() as session: query = self._construct_unsolved_python_package_versions_query( session, os_name=os_name, os_version=os_version, python_version=python_version ) query = query.join(PythonPackageIndex).with_entities( PythonPackageVersionEntity.package_name, PythonPackageIndex.url ) query = query.offset(start_offset).limit(count) if distinct: query = query.distinct() return query.all()
[docs] def get_unsolved_python_packages_all_versions( self, *, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, start_offset: int = 0, count: Optional[int] = DEFAULT_COUNT, distinct: bool = False, ) -> Dict[str, List[Tuple[str, str]]]: """Retrieve unsolved Python package versions per package in Thoth Database. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_unsolved_python_packages_all_versions() {'absl-py': [('0.1.10', 'https://pypi.org/simple'), ('0.2.1', 'https://pypi.org/simple')]} """ os_name = map_os_name(os_name) os_version = normalize_os_version(os_name, os_version) with self._session_scope() as session: query = self._construct_unsolved_python_package_versions_query( session, os_name=os_name, os_version=os_version, python_version=python_version ) query = ( query.join(PythonPackageIndex) .with_entities( PythonPackageVersionEntity.package_name, PythonPackageVersionEntity.package_version, PythonPackageIndex.url, ) .group_by( PythonPackageVersionEntity.package_name, PythonPackageVersionEntity.package_version, PythonPackageIndex.url, ) ) query = query.offset(start_offset).limit(count) if distinct: query = query.distinct() result = query.all() return self._group_by_package_name(result=result)
[docs] def get_unsolved_python_package_versions_count( self, *, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, start_offset: int = 0, count: Optional[int] = DEFAULT_COUNT, distinct: bool = False, ) -> Dict[Tuple[str, str, str], int]: """Retrieve number of unsolved versions per Python package in Thoth Database. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_unsolved_python_package_versions_count() {('absl-py', '0.1.10', 'https://pypi.org/simple'): 1, ('absl-py', '0.2.1', 'https://pypi.org/simple'): 1} """ os_name = map_os_name(os_name) os_version = normalize_os_version(os_name, os_version) with self._session_scope() as session: query = self._construct_unsolved_python_package_versions_query( session, os_name=os_name, os_version=os_version, python_version=python_version ) query = ( query.join(PythonPackageIndex) .with_entities( PythonPackageVersionEntity.package_name, PythonPackageVersionEntity.package_version, PythonPackageIndex.url, func.count( tuple_( PythonPackageVersionEntity.package_name, PythonPackageVersionEntity.package_version, PythonPackageIndex.url, ) ), ) .group_by( PythonPackageVersionEntity.package_name, PythonPackageVersionEntity.package_version, PythonPackageIndex.url, ) ) query = query.offset(start_offset).limit(count) if distinct: query = query.distinct() result = query.all() return self._count_per_package(result=result)
[docs] def get_unsolved_python_package_versions_count_per_index( self, index_url: str, *, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, start_offset: int = 0, count: Optional[int] = DEFAULT_COUNT, distinct: bool = False, ) -> Dict[str, Dict[Tuple[str, str], int]]: """Retrieve number of unsolved Python package versions per index url in Thoth Database. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_unsolved_python_package_versions_count_per_index(index_url='https://pypi.org/simple') {'https://pypi.org/simple': {('absl-py', '0.1.10'): 1, ('absl-py', '0.2.1'): 1}} """ os_name = map_os_name(os_name) os_version = normalize_os_version(os_name, os_version) with self._session_scope() as session: query = self._construct_unsolved_python_package_versions_query( session, index_url=index_url, os_name=os_name, os_version=os_version, python_version=python_version ) query = ( query.join(PythonPackageIndex) .with_entities( PythonPackageVersionEntity.package_name, PythonPackageVersionEntity.package_version, PythonPackageIndex.url, func.count( tuple_( PythonPackageVersionEntity.package_name, PythonPackageVersionEntity.package_version, PythonPackageIndex.url, ) ), ) .group_by( PythonPackageVersionEntity.package_name, PythonPackageVersionEntity.package_version, PythonPackageIndex.url, ) ) query = query.offset(start_offset).limit(count) if distinct: query = query.distinct() result = query.all() return self._count_per_index(result=result, index_url=index_url)
[docs] def get_unsolved_python_package_versions_count_per_version( self, package_name: str, *, start_offset: int = 0, count: Optional[int] = DEFAULT_COUNT, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, distinct: bool = False, ) -> Dict[str, Dict[str, int]]: """Retrieve number of unsolved Python package versions per package version in Thoth Database. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_unsolved_python_package_versions_count_per_version(package_name='tensorflow') {'1.14.0rc0': {'https://pypi.org/simple': 1}, '1.13.0rc2': {'https://pypi.org/simple': 1}} """ os_name = map_os_name(os_name) os_version = normalize_os_version(os_name, os_version) with self._session_scope() as session: query = self._construct_unsolved_python_package_versions_query( session, package_name=package_name, os_name=os_name, os_version=os_version, python_version=python_version, ) query = ( query.join(PythonPackageIndex) .with_entities( PythonPackageVersionEntity.package_name, PythonPackageVersionEntity.package_version, PythonPackageIndex.url, func.count( tuple_( PythonPackageVersionEntity.package_name, PythonPackageVersionEntity.package_version, PythonPackageIndex.url, ) ), ) .group_by( PythonPackageVersionEntity.package_name, PythonPackageVersionEntity.package_version, PythonPackageIndex.url, ) ) query = query.offset(start_offset).limit(count) if distinct: query = query.distinct() result = query.all() return self._count_per_version(result=result)
[docs] def get_unsolved_python_package_versions_all( self, package_name: Optional[str] = None, package_version: Optional[str] = None, index_url: Optional[str] = None, *, start_offset: int = 0, count: Optional[int] = DEFAULT_COUNT, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, distinct: bool = False, randomize: bool = True, ) -> List[Tuple[str, Optional[str], Optional[str]]]: """Retrieve unsolved Python package versions in Thoth Database. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_unsolved_python_package_versions_all() [('regex', '2018.11.7', 'https://pypi.org/simple'), ('tensorflow', '1.11.0', 'https://pypi.org/simple')] """ os_name = map_os_name(os_name) os_version = normalize_os_version(os_name, os_version) with self._session_scope() as session: query = self._construct_unsolved_python_package_versions_query( session, package_name=package_name, package_version=package_version, index_url=index_url, os_name=os_name, os_version=os_version, python_version=python_version, ) query = query.join(PythonPackageIndex).with_entities( PythonPackageVersionEntity.package_name, PythonPackageVersionEntity.package_version, PythonPackageIndex.url, ) if randomize: query = query.order_by(func.random()) query = query.offset(start_offset).limit(count) if distinct: query = query.distinct() return query.all()
[docs] def get_unsolved_python_package_versions_count_all( self, package_name: Optional[str] = None, package_version: Optional[str] = None, index_url: Optional[str] = None, *, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, distinct: bool = False, ) -> int: """Retrieve unsolved Python package versions number in Thoth Database.""" os_name = map_os_name(os_name) os_version = normalize_os_version(os_name, os_version) with self._session_scope() as session: query = self._construct_unsolved_python_package_versions_query( session, package_name=package_name, package_version=package_version, index_url=index_url, os_name=os_name, os_version=os_version, python_version=python_version, ) query = query.join(PythonPackageIndex).with_entities( PythonPackageVersionEntity.package_name, PythonPackageVersionEntity.package_version, PythonPackageIndex.url, ) if distinct: query = query.distinct() return query.count()
# SI Analyzed Python Packages def _construct_si_analyzed_python_package_versions_query(self, session: Session) -> Query: """Construct query for packages analyzed by solver and analyzed by SI.""" query = session.query(SecurityIndicatorAggregatedRun) # We find all rows that are same in PythonPackageVersion and SIAggregated table. conditions = [ SIAggregated.python_package_version_id == PythonPackageVersion.id, PythonPackageVersion.python_package_index_id == PythonPackageIndex.id, ] query = query.filter(exists().where(and_(*conditions))) return query
[docs] def get_si_analyzed_python_package_versions_all( self, *, distinct: bool = False, ) -> List[Tuple[str, str, str]]: """Get SI analyzed Python package versions in Thoth Database. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_si_analyzed_python_package_versions_all() [('fbprophet', '0.4', 'https://pypi.org/simple')] """ with self._session_scope() as session: query = self._construct_si_analyzed_python_package_versions_query(session) query = query.with_entities( PythonPackageVersion.package_name, PythonPackageVersion.package_version, PythonPackageIndex.url, ) if distinct: query = query.distinct() return query.all()
[docs] def get_si_analyzed_python_package_versions_count_all( self, *, distinct: bool = False, ) -> int: """Get SI analyzed Python package versions number in Thoth Database.""" with self._session_scope() as session: query = self._construct_si_analyzed_python_package_versions_query(session) query = query.with_entities( PythonPackageVersion.package_name, PythonPackageVersion.package_version, PythonPackageIndex.url, ) if distinct: query = query.distinct() return query.count()
def _construct_si_unanalyzed_python_package_versions_query( self, session: Session, index_url: Optional[str] = None, provides_source_distro: bool = True, si_error: bool = False, ) -> Query: """Construct query for packages analyzed by solver, but unanalyzed by SI.""" index_url = self.normalize_python_index_url(index_url) query = session.query(PythonPackageVersion).filter( PythonPackageVersion.package_version.isnot(None), PythonPackageIndex.url.isnot(None), PythonPackageIndex.enabled.is_(True), PythonPackageVersion.provides_source_distro.is_(provides_source_distro), ) if index_url is not None: query = query.filter(PythonPackageIndex.url == index_url) # We find all rows that are same in PythonPackageVersion and SIAggregated table. conditions = [ PythonPackageVersion.entity_id == SIAggregated.python_package_version_entity_id, SIAggregated.si_aggregated_run_id == SecurityIndicatorAggregatedRun.id, ] # Finally filter these out. query = query.filter(~exists().where(and_(*conditions))) query = query.filter(exists().where(SecurityIndicatorAggregatedRun.error.is_(si_error))) return query
[docs] def get_si_unanalyzed_python_package_versions_all( self, start_offset: int = 0, count: Optional[int] = DEFAULT_COUNT, distinct: bool = True, randomize: bool = True, provides_source_distro: bool = True, si_error: bool = False, ) -> List[Tuple[str, str, str]]: """Retrieve solved Python package versions in Thoth Database, that are not anaylyzed by SI. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_si_unanalyzed_python_package_versions_all() [('crossbar', '0.10.0', 'https://pypi.org/simple'), ('tensorflow', '1.11.0', 'https://pypi.org/simple')] """ with self._session_scope() as session: query = self._construct_si_unanalyzed_python_package_versions_query( session, provides_source_distro=provides_source_distro, si_error=si_error, ) query = query.join(PythonPackageIndex).with_entities( PythonPackageVersion.package_name, PythonPackageVersion.package_version, PythonPackageIndex.url, ) if randomize: query = query.order_by(func.random()) query = query.offset(start_offset).limit(count) if distinct: query = query.distinct() return query.all()
[docs] def get_si_unanalyzed_python_package_versions_count_all( self, index_url: Optional[str] = None, *, distinct: bool = False, provides_source_distro: bool = True, si_error: bool = False, ) -> int: """Get SI unanalyzed Python package versions number in Thoth Database.""" with self._session_scope() as session: query = self._construct_si_unanalyzed_python_package_versions_query( session, provides_source_distro=provides_source_distro, si_error=si_error, ) query = query.join(PythonPackageIndex).with_entities( PythonPackageVersion.package_name, PythonPackageVersion.package_version, PythonPackageIndex.url, ) if distinct: query = query.distinct() return query.count()
def _construct_get_solver_query(self, session: Session) -> Query: """Construct query to retrieve solvers.""" query = session.query(EcosystemSolver).distinct(EcosystemSolver.solver_name) return query
[docs] def get_ecosystem_solver_all(self) -> List[str]: """Get all solvers. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_ecosystem_solver_all() ['solver-fedora-31-py38', 'solver-fedora-32-py37', 'solver-fedora-32-py38', 'solver-ubi-8-py36'] """ with self._session_scope() as session: query = self._construct_get_solver_query( session, ) solvers = query.with_entities(EcosystemSolver.solver_name).all() return [s[0] for s in solvers]
[docs] def get_ecosystem_solver_count_all(self) -> int: """Get number of solvers.""" with self._session_scope() as session: query = self._construct_get_solver_query( session, ) return query.count()
[docs] def get_solver_documents_count_all(self) -> int: """Get number of solver documents synced into graph.""" with self._session_scope() as session: return session.query(Solved).distinct(Solved.document_id).count()
[docs] def get_analyzer_documents_count_all(self) -> int: """Get number of image analysis documents synced into graph.""" with self._session_scope() as session: return session.query(PackageExtractRun).distinct(PackageExtractRun.analysis_document_id).count()
def _construct_query_get_si_aggregated_python_package_version( self, session: Session, package_name: Optional[str], package_version: Optional[str], index_url: Optional[str] ) -> Query: """Construct query for aggregate Security Indicators (SI) results per Python package version functions, the query is not executed. """ query = session.query(SecurityIndicatorAggregatedRun) if package_name is not None: package_name = self.normalize_python_package_name(package_name) query = query.filter(PythonPackageVersion.package_name == package_name) if package_version is not None: package_version = self.normalize_python_package_version(package_version) query = query.filter(PythonPackageVersion.package_version == package_version) if index_url is not None: index_url = self.normalize_python_index_url(index_url) query = query.filter(PythonPackageIndex.url == index_url) query = query.with_entities(SecurityIndicatorAggregatedRun) query = query.filter( PythonPackageVersion.id == SIAggregated.python_package_version_id, ) return query
[docs] def si_aggregated_python_package_version_exists( self, package_name: str, package_version: str, index_url: str ) -> bool: """Check if Aggregate Security Indicators (SI) results exists for Python package version.""" index_url = self.normalize_python_index_url(index_url) with self._session_scope() as session: query = self._construct_query_get_si_aggregated_python_package_version( session=session, package_name=package_name, package_version=package_version, index_url=index_url ) return query.count() > 0
[docs] @lru_cache(maxsize=_GET_SI_AGGREGATED_PYTHON_PACKAGE_VERSION_CACHE_SIZE) def get_si_aggregated_python_package_version( self, package_name: str, package_version: str, index_url: str ) -> Dict[str, int]: """Get Aggregate Security Indicators (SI) results per Python package version. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_si_aggregated_python_package_version( package_name='thoth-common', package_version='0.10.0', index_url='https://pypi.org/simple' ) { 'severity_high_confidence_high': 0, 'severity_high_confidence_low': 0, 'severity_high_confidence_medium': 0, 'severity_high_confidence_undefined': 0, 'severity_low_confidence_high': 0, 'severity_low_confidence_low': 0, 'severity_low_confidence_medium': 0, 'severity_low_confidence_undefined': 0, 'severity_medium_confidence_high': 0, 'severity_medium_confidence_low': 0, 'severity_medium_confidence_medium': 0, 'severity_medium_confidence_undefined': 0, 'number_of_analyzed_files': 0, 'number_of_files_total': 0, 'number_of_files_with_severities': 0, 'number_of_filtered_files': 0, 'number_of_python_files': 39, 'number_of_lines_with_comments_in_python_files': 922, 'number_of_blank_lines_in_python_files': 2760, 'number_of_lines_with_code_in_python_files': 9509, 'total_number_of_files': 75, 'total_number_of_lines': 36856, 'total_number_of_lines_with_comments': 2895, 'total_number_of_blank_lines': 6737, 'total_number_of_lines_with_code': 27224 } """ index_url = self.normalize_python_index_url(index_url) with self._session_scope() as session: query = self._construct_query_get_si_aggregated_python_package_version( session=session, package_name=package_name, package_version=package_version, index_url=index_url ) result = query.order_by(SecurityIndicatorAggregatedRun.datetime.desc()).first() if result is None: raise NotFoundError( f"No record found for {package_name!r} in version {package_version!r} from {index_url!r}" ) result = result.to_dict() result.pop("si_aggregated_run_document_id") result.pop("datetime") return result
[docs] def retrieve_dependent_packages( self, package_name: str, package_version: Optional[str] = None ) -> Dict[str, List[str]]: """Get mapping package name to package version of packages that depend on the given package.""" package_name = self.normalize_python_package_name(package_name) package_version = self.normalize_python_package_version(package_version) with self._session_scope() as session: query = session.query(PythonPackageVersionEntity).filter( PythonPackageVersionEntity.package_name == package_name ) if package_version is not None: query = query.filter(PythonPackageVersionEntity.package_version == package_version) query_result = ( query.join(DependsOn) .join(PythonPackageVersion) .with_entities(PythonPackageVersion.package_name, PythonPackageVersion.package_version) .distinct() .all() ) result = {} for package_name, package_version in query_result: if package_name not in result: result[package_name] = [] result[package_name].append(package_version) return result
[docs] @lru_cache(maxsize=_GET_PYTHON_PACKAGE_VERSION_RECORDS_CACHE_SIZE) def get_python_package_version_records( self, package_name: str, package_version: str, index_url: Union[str, None], *, os_name: Union[str, None], os_version: Union[str, None], python_version: Union[str, None], ) -> List[dict]: """Get records for the given package regardless of index_url.""" package_name = self.normalize_python_package_name(package_name) package_version = self.normalize_python_package_version(package_version) with self._session_scope() as session: query = session.query(PythonPackageVersion).filter_by( package_name=package_name, package_version=package_version ) if os_name is not None: os_name = map_os_name(os_name) query = query.filter(PythonPackageVersion.os_name == os_name) if os_version is not None: os_version = normalize_os_version(os_name, os_version) query = query.filter(PythonPackageVersion.os_version == os_version) if python_version is not None: query = query.filter(PythonPackageVersion.python_version == python_version) query = query.join(PythonPackageIndex) if index_url is not None: index_url = self.normalize_python_index_url(index_url) query = query.filter(PythonPackageIndex.url == index_url) query_result = ( query.with_entities( PythonPackageVersion.package_name, PythonPackageVersion.package_version, PythonPackageIndex.url, PythonPackageVersion.os_name, PythonPackageVersion.os_version, PythonPackageVersion.python_version, ) .distinct() .all() ) result = [] for item in query_result: result.append( { "package_name": item[0], "package_version": item[1], "index_url": item[2], "os_name": item[3], "os_version": item[4], "python_version": item[5], } ) return result
[docs] def retrieve_transitive_dependencies_python( self, package_name: str, package_version: str, index_url: str, *, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, extras: FrozenSet[Optional[str]] = None, marker_evaluation_result: Optional[bool] = None, ) -> List[ Tuple[ Tuple[str, str, str], Tuple[str, str, str], Tuple[str, str, str], Tuple[str, str, str], Union[Tuple[str, str, str], None], Union[Tuple[str, str, str], None], ] ]: """Get all transitive dependencies for the given package by traversing dependency graph. It's much faster to retrieve just dependency ids for the transitive dependencies as most of the time is otherwise spent in serialization and deserialization of query results. The ids are obtained later on (kept in ids map, see bellow). The ids map represents a map to optimize number of retrievals - not to perform duplicate queries into graph instance. Extras are taken into account only for direct dependencies. Any extras required in libraries used in transitive dependencies are not required as solver directly report dependencies regardless extras configuration - see get_depends_on docs for extras parameter values.. """ index_url = self.normalize_python_index_url(index_url) package_name = self.normalize_python_package_name(package_name) package_version = self.normalize_python_package_version(package_version) result = [] initial_stack_entry = (extras, package_name, package_version, index_url) stack = deque((initial_stack_entry,)) seen_tuples = {(package_name, package_version, index_url)} while stack: ( extras, package_name, package_version, index_url, ) = stack.pop() package_tuple = (package_name, package_version, index_url) configurations = self.get_python_package_version_records( package_name=package_name, package_version=package_version, index_url=index_url, os_name=os_name, os_version=os_version, python_version=python_version, ) for configuration in configurations: dependencies = self.get_depends_on( package_name=configuration["package_name"], package_version=configuration["package_version"], index_url=configuration["index_url"], os_name=configuration["os_name"], os_version=configuration["os_version"], python_version=configuration["python_version"], extras=extras, marker_evaluation_result=marker_evaluation_result, ) for dependency_name, dependency_version in itertools.chain(*dependencies.values()): records = self.get_python_package_version_records( package_name=dependency_name, package_version=dependency_version, index_url=None, # Do cross-index resolution... os_name=configuration["os_name"], os_version=configuration["os_version"], python_version=configuration["python_version"], ) if not records: # Not resolved yet. result.append((package_tuple, (dependency_name, dependency_version, None))) else: for record in records: dependency_tuple = (record["package_name"], record["package_version"], record["index_url"]) result.append((package_tuple, dependency_tuple)) if dependency_tuple not in seen_tuples: # Explicitly set extras to None as we do not have direct dependency anymore. stack.append((None, *dependency_tuple)) seen_tuples.add(dependency_tuple) return result
[docs] @lru_cache(maxsize=_GET_PYTHON_ENVIRONMENT_MARKER_CACHE_SIZE) def get_python_environment_marker( self, package_name: str, package_version: str, index_url: str, *, dependency_name: str, dependency_version: str, os_name: str, os_version: str, python_version: str, ) -> Optional[str]: """Get Python evaluation marker as per PEP-0508. @raises NotFoundError: if the given package has no entry in the database """ index_url = self.normalize_python_index_url(index_url) package_name = self.normalize_python_package_name(package_name) package_version = self.normalize_python_package_version(package_version) os_name = map_os_name(os_name) os_version = normalize_os_version(os_name, os_version) with self._session_scope() as session: result = ( session.query(PythonPackageVersion) .filter(PythonPackageVersion.package_name == package_name) .filter(PythonPackageVersion.package_version == package_version) .filter(PythonPackageVersion.os_name == os_name) .filter(PythonPackageVersion.os_version == os_version) .filter(PythonPackageVersion.python_version == python_version) .join(PythonPackageIndex) .filter(PythonPackageIndex.url == index_url) .join(DependsOn) .join(PythonPackageVersionEntity) .filter(PythonPackageVersionEntity.package_name == dependency_name) .filter(PythonPackageVersionEntity.package_version == dependency_version) .with_entities(DependsOn.marker) .first() ) if result is None: raise NotFoundError( f"No records found for package {(package_name, package_version, index_url)!r} with " f"dependency {(dependency_name, dependency_version)!r} running on {os_name!r} in version " f"{os_version!r} using Python in version {python_version!r}" ) return result[0]
[docs] def get_python_environment_marker_evaluation_result( self, package_name: str, package_version: str, index_url: str, *, dependency_name: str, dependency_version: str, os_name: str, os_version: str, python_version: str, ) -> bool: """Get result of the Python evaluation marker. The `extra` part of the environment marker (an exception in PEP-0508) is not taken into account and is substituted with a value which always defaults to True (as it would cause an error during context interpreting). See solver implementation for details. @raises NotFoundError: if the given package has no entry in the database """ package_name = self.normalize_python_package_name(package_name) package_version = self.normalize_python_package_version(package_version) os_name = map_os_name(os_name) os_version = normalize_os_version(os_name, os_version) index_url = self.normalize_python_index_url(index_url) with self._session_scope() as session: result = ( session.query(PythonPackageVersion) .filter(PythonPackageVersion.package_name == package_name) .filter(PythonPackageVersion.package_version == package_version) .filter(PythonPackageVersion.os_name == os_name) .filter(PythonPackageVersion.os_version == os_version) .filter(PythonPackageVersion.python_version == python_version) .join(PythonPackageIndex) .filter(PythonPackageIndex.url == index_url) .join(DependsOn) .join(PythonPackageVersionEntity) .filter(PythonPackageVersionEntity.package_name == dependency_name) .filter(PythonPackageVersionEntity.package_version == dependency_version) .with_entities(DependsOn.marker_evaluation_result) .first() ) if result is None: raise NotFoundError( f"No records found for package {(package_name, package_version, index_url)!r} with " f"dependency {(dependency_name, dependency_version)!r} running on {os_name!r} in version " f"{os_version!r} using Python in version {python_version!r}" ) return result[0]
[docs] def get_python_package_version_dependents_all( self, package_name: str, *, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, start_offset: int = 0, count: int = DEFAULT_COUNT, ) -> List[Dict[str, Any]]: """Get dependents for the given package. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_dependents("selinon", os_name="rhel", os_version="8", python_version="3.6") [ { "index_url": "https://pypi.org/simple", "package_name": "thoth-worker", "package_version": "0.0.2", "version_range": ">=1.0.0", "marker_evaluation_result": True, "marker": None, "extra": None, } ] """ package_name = self.normalize_python_package_name(package_name) with self._session_scope() as session: query = ( session.query(PythonPackageVersionEntity) .filter(PythonPackageVersionEntity.package_name == package_name) .join(DependsOn) ) query = query.join(PythonPackageVersion) if os_name is not None: os_name = map_os_name(os_name) query = query.filter(PythonPackageVersion.os_name == os_name) if os_version is not None: os_version = normalize_os_version(os_name, os_version) query = query.filter(PythonPackageVersion.os_version == os_version) if python_version is not None: query = query.filter(PythonPackageVersion.python_version == python_version) query_result = ( query.distinct() .join(PythonPackageIndex) .offset(start_offset) .limit(count) .with_entities( PythonPackageVersion.package_name, PythonPackageVersion.package_version, PythonPackageIndex.url, DependsOn.version_range, DependsOn.marker_evaluation_result, DependsOn.marker, DependsOn.extra, ) .all() ) result = [] for entry in query_result: result.append( { "package_name": entry[0], "package_version": entry[1], "index_url": entry[2], "version_range": entry[3], "marker_evaluation_result": entry[4], "marker": entry[5], "extra": entry[6], } ) return result
[docs] @staticmethod def python_package_version_depends_on_platform_exists(platform: str) -> bool: """Check if the given platform has some records in the database.""" return platform in (p.value for p in PlatformEnum)
[docs] @staticmethod def get_python_package_version_platform_all() -> List[str]: """Retrieve all platforms stored in the database. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_python_package_version_platform_all() ['linux-x86_64'] """ return [p.value for p in PlatformEnum]
[docs] @lru_cache(maxsize=_GET_DEPENDS_ON_CACHE_SIZE) def get_depends_on( self, package_name: str, package_version: Optional[str] = None, index_url: Optional[str] = None, *, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, extras: FrozenSet[Optional[str]] = None, marker_evaluation_result: Optional[bool] = None, is_missing: Optional[bool] = None, ) -> Dict[str, List[Tuple[str, str]]]: """Get dependencies for the given Python package respecting environment and extras. If no environment is provided, dependencies are returned for all environments as stored in the database. Extras (as described in PEP-0508) are respected. If no extras is provided (extras=None), all dependencies are returned with all extras specified. A special value of None in extras listing no extra: * extras=frozenset((None,)) - return only dependencies which do not have any extra assigned * extras=frozenset((None, "postgresql")) - dependencies without extra and with extra "postgresql" * extras=None - return all dependencies (regardless extra) Environment markers are not taken into account in this query. """ package_name = self.normalize_python_package_name(package_name) if package_version is not None: package_version = self.normalize_python_package_version(package_version) if index_url is not None: index_url = self.normalize_python_index_url(index_url) if os_name is not None: os_name = map_os_name(os_name) if os_version is not None: os_version = normalize_os_version(os_name, os_version) package_requested = locals() package_requested.pop("self") with self._session_scope() as session: query = session.query(PythonPackageVersion).filter(PythonPackageVersion.package_name == package_name) if package_version is not None: query = query.filter(PythonPackageVersion.package_version == package_version) if os_name is not None: query = query.filter(PythonPackageVersion.os_name == os_name) if os_version is not None: query = query.filter(PythonPackageVersion.os_version == os_version) if python_version is not None: query = query.filter(PythonPackageVersion.python_version == python_version) if is_missing is not None: query = query.filter(PythonPackageVersion.is_missing == is_missing) if index_url is not None: query = query.join(PythonPackageIndex).filter(PythonPackageIndex.url == index_url) # Mark the query here for later check, if we do not have any records for the given # package for the given environment. package_query = query query = query.join(DependsOn) if extras: # We cannot use in_ here as sqlalchemy does not support None in the list. query = query.filter(or_(*(DependsOn.extra == i for i in extras))) if marker_evaluation_result is not None: query = query.filter(DependsOn.marker_evaluation_result == marker_evaluation_result) dependencies = ( query.join(PythonPackageVersionEntity) .with_entities( DependsOn.extra, PythonPackageVersionEntity.package_name, PythonPackageVersionEntity.package_version ) .distinct() .all() ) if not dependencies: if package_query.count() == 0: raise NotFoundError(f"No package record for {package_requested!r} found") result = {} for dependency in dependencies: extra, package_name, package_version = dependency if extra not in result: result[extra] = [] result[extra].append((package_name, package_version)) return result
[docs] def retrieve_transitive_dependencies_python_multi( self, *package_tuples, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, ) -> Dict[ Tuple[str, str, str], Set[ Tuple[ Tuple[str, str, str], Tuple[str, str, str], Tuple[str, str, str], Tuple[str, str, str], Union[Tuple[str, str, str], None], Union[Tuple[str, str, str], None], ] ], ]: """Get all transitive dependencies for a given set of packages by traversing the dependency graph.""" result = {} for package_tuple in package_tuples: result[package_tuple] = self.retrieve_transitive_dependencies_python( *package_tuple, os_name=os_name, os_version=os_version, python_version=python_version ) return result
[docs] def solver_records_exist(self, solver_document: dict) -> bool: """Check if the given solver document record exists.""" solver_document_id = SolverResultsStore.get_document_id(solver_document) return self.solver_document_id_exist(solver_document_id)
[docs] def solver_document_id_exists(self, solver_document_id: str) -> bool: """Check if there is a solver document record with the given id.""" with self._session_scope() as session: return session.query(Solved).filter(Solved.document_id == solver_document_id).count() > 0
[docs] def dependency_monkey_document_id_exists(self, dependency_monkey_document_id: str) -> bool: """Check if the given dependency monkey report record exists in the graph database.""" with self._session_scope() as session: return ( session.query(DependencyMonkeyRun) .filter(DependencyMonkeyRun.dependency_monkey_document_id == dependency_monkey_document_id) .count() > 0 )
[docs] def si_aggregated_document_id_exists(self, si_aggregated_run_document_id: str) -> bool: """Check if the given security indicator aggregated report record exists in the graph database.""" with self._session_scope() as session: return ( session.query(SecurityIndicatorAggregatedRun) .filter(SecurityIndicatorAggregatedRun.si_aggregated_run_document_id == si_aggregated_run_document_id) .count() > 0 )
[docs] def inspection_document_id_result_number_exists( self, inspection_document_id: str, inspection_result_number: int ) -> bool: """Check if the given inspection id result number record exists in the graph database.""" with self._session_scope() as session: return ( session.query(InspectionRun) .filter(InspectionRun.inspection_document_id == inspection_document_id) .filter(InspectionRun.inspection_result_number == inspection_result_number) .count() > 0 )
[docs] def adviser_document_id_exist(self, adviser_document_id: str) -> bool: """Check if there is a adviser document record with the given id.""" with self._session_scope() as session: return session.query(AdviserRun).filter(AdviserRun.adviser_document_id == adviser_document_id).count() > 0
[docs] def analysis_records_exist(self, analysis_document: dict) -> bool: """Check whether the given analysis document records exist in the graph database.""" analysis_document_id = AnalysisResultsStore.get_document_id(analysis_document) return self.analysis_document_id_exist(analysis_document_id)
[docs] def analysis_document_id_exist(self, analysis_document_id: str) -> bool: """Check if there is an analysis document record with the given id.""" with self._session_scope() as session: return ( session.query(PackageExtractRun) .filter(PackageExtractRun.analysis_document_id == analysis_document_id) .count() > 0 )
[docs] def get_last_analysis_document_id( self, thoth_s2i_image_name: str, thoth_s2i_image_version: str, *, is_external: bool = False ) -> Optional[Dict[str, str]]: """Get last image analysis (if any) for the given container image.""" model = ExternalSoftwareEnvironment if is_external else SoftwareEnvironment with self._session_scope() as session: result = ( session.query(PackageExtractRun) .filter(model.thoth_s2i_image_name == thoth_s2i_image_name) .filter(model.thoth_s2i_image_version == thoth_s2i_image_version) .order_by(PackageExtractRun.datetime.desc()) .with_entities(PackageExtractRun.analysis_document_id) .first() ) if not result: return None return result[0]
[docs] def inspection_document_id_exist(self, inspection_document_id: str) -> bool: """Check if there is an inspection document record with the given id.""" with self._session_scope() as session: return ( session.query(InspectionRun) .filter(InspectionRun.inspection_document_id == inspection_document_id) .count() > 0 )
[docs] def provenance_checker_document_id_exist(self, provenance_checker_document_id: str) -> bool: """Check if there is a provenance-checker document record with the given id.""" with self._session_scope() as session: return ( session.query(ProvenanceCheckerRun) .filter(ProvenanceCheckerRun.provenance_checker_document_id == provenance_checker_document_id) .count() > 0 )
[docs] @lru_cache(maxsize=_GET_PYTHON_CVE_RECORDS_ALL_CACHE_SIZE) def get_python_cve_records_all(self, package_name: str, package_version: Optional[str] = None) -> List[dict]: """Get known vulnerabilities for the given package-version.""" package_name = self.normalize_python_package_name(package_name) if package_version: package_version = self.normalize_python_package_version(package_version) with self._session_scope() as session: query = session.query(PythonPackageVersionEntity).filter( PythonPackageVersionEntity.package_name == package_name ) if package_version: query = query.filter(PythonPackageVersionEntity.package_version == package_version) result = query.join(HasVulnerability).join(CVE).with_entities(CVE).distinct().all() return [cve.to_dict() for cve in result]
[docs] def get_python_cve_records_count(self) -> int: """Get number of CVE in Thoth database.""" with self._session_scope() as session: return session.query(CVE.id).count()
[docs] def get_python_package_hashes_sha256( self, package_name: str, package_version: str, index_url: str, *, distinct: bool = False ) -> List[str]: """Get all hashes for Python package in Thoth Database. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_python_package_hashes_sha256() [ '9d6863f6c70d034b8c34b3355cb7ba7d2ad799583947265efda41fe67127c23f', '8e4a1f6d89cfaadb486237acbfa24700add01da022dfcf3536e5071d21e13ee0' ] """ package_name = self.normalize_python_package_name(package_name) package_version = self.normalize_python_package_version(package_version) index_url = self.normalize_python_index_url(index_url) with self._session_scope() as session: query = ( session.query(PythonPackageVersionEntity) .filter(PythonPackageVersionEntity.package_name == package_name) .filter(PythonPackageVersionEntity.package_version == package_version) .join(PythonPackageIndex) .filter(PythonPackageIndex.url == index_url) .join(HasArtifact) .join(PythonArtifact) .with_entities(PythonArtifact.artifact_hash_sha256) ) if distinct: query = query.distinct() result = query.all() return [item[0] for item in result]
[docs] def is_python_package_index_enabled(self, url: str) -> bool: """Check if the given Python package index is enabled.""" with self._session_scope() as session: result = session.query(PythonPackageIndex.enabled).filter_by(url=url).first() if result is None: raise NotFoundError(f"No records for Python package index with URL {url!r} found") return result[0]
[docs] def set_python_package_index_state(self, url: str, *, enabled: bool) -> None: """Enable or disable Python package index.""" session = self._sessionmaker() try: with session.begin(subtransactions=True): python_package_index = session.query(PythonPackageIndex).filter(PythonPackageIndex.url == url).first() if python_package_index is None: raise NotFoundError(f"Python package index {url!r} not found") python_package_index.enabled = enabled session.add(python_package_index) except Exception: session.rollback() raise else: session.commit()
[docs] def register_python_package_index( self, url: str, warehouse_api_url: Optional[str] = None, verify_ssl: bool = True, enabled: bool = False, only_if_package_seen: bool = True, ) -> bool: """Register the given Python package index in the graph database.""" with self._session_scope() as session: python_package_index = session.query(PythonPackageIndex).filter(PythonPackageIndex.url == url).first() if python_package_index is None: PythonPackageIndex.get_or_create( session=session, url=url, warehouse_api_url=warehouse_api_url, verify_ssl=verify_ssl, enabled=enabled, only_if_package_seen=only_if_package_seen, ) return True else: insert_stmt = insert(PythonPackageIndex).values(**python_package_index.to_dict(without_id=False)) do_update_stmt = insert_stmt.on_conflict_do_update( index_elements=["id"], set_=dict( warehouse_api_url=warehouse_api_url, verify_ssl=verify_ssl, enabled=enabled, only_if_package_seen=only_if_package_seen, ), ) session.execute(do_update_stmt) return False
[docs] def delete_python_package_index(self, index_url: str) -> None: """Delete the given Python package index.""" with self._session_scope() as session: return session.query(PythonPackageIndex).filter(PythonPackageIndex.url == index_url).delete()
[docs] def get_python_package_index_all(self, enabled: bool = None) -> List[Dict[str, Any]]: """Get listing of Python package indexes registered in the graph database.""" with self._session_scope() as session: query = session.query( PythonPackageIndex.url, PythonPackageIndex.warehouse_api_url, PythonPackageIndex.verify_ssl, PythonPackageIndex.only_if_package_seen, ) if enabled is not None: query = query.filter(PythonPackageIndex.enabled == enabled) return [ {"url": item[0], "warehouse_api_url": item[1], "verify_ssl": item[2], "only_if_package_seen": item[3]} for item in query.all() ]
[docs] def get_hardware_environments_all( self, is_external: bool = False, *, start_offset: int = 0, count: Optional[int] = DEFAULT_COUNT, without_id: bool = True, ) -> List[Dict]: """Get hardware environments (external or internal) registered in the graph database.""" if is_external: hardware_environment = ExternalHardwareInformation else: hardware_environment = HardwareInformation with self._session_scope() as session: result = session.query(hardware_environment).offset(start_offset).limit(count).all() return [model.to_dict(without_id=without_id) for model in result]
[docs] def get_software_environments_all( self, is_external: bool = False, *, start_offset: int = 0, count: Optional[int] = DEFAULT_COUNT, env_image_name: Optional[str] = None, env_image_tag: Optional[str] = None, ) -> List[Dict]: """Get software environments (external or internal) registered in the graph database.""" if is_external: software_environment = ExternalSoftwareEnvironment else: software_environment = SoftwareEnvironment with self._session_scope() as session: query = session.query(software_environment) if env_image_name: query = query.filter(software_environment.env_image_name == env_image_name) if env_image_tag: query = query.filter(software_environment.env_image_tag == env_image_tag) query = query.offset(start_offset).limit(count) return [model.to_dict() for model in query.all()]
[docs] def get_python_package_index_urls_all(self, enabled: Optional[bool] = None) -> List[str]: """Retrieve all the URLs of registered Python package indexes.""" with self._session_scope() as session: query = session.query(PythonPackageIndex) if enabled is not None: query = query.filter(PythonPackageIndex.enabled == enabled) return [item[0] for item in query.with_entities(PythonPackageIndex.url).distinct().all()]
[docs] def get_python_package_versions_per_index(self, index_url: str, *, distinct: bool = False) -> Dict[str, List[str]]: """Retrieve listing of Python packages (solved) known to graph database instance for the given index.""" index_url = self.normalize_python_index_url(index_url) with self._session_scope() as session: query = ( session.query(PythonPackageVersion) .join(PythonPackageIndex) .filter(PythonPackageIndex.url == index_url) .with_entities(PythonPackageVersion.package_name) ) if distinct: query = query.distinct() query = query.all() return {index_url: [item[0] for item in query]}
[docs] def get_python_package_version_entities_count_all(self, *, distinct: bool = False) -> int: """Retrieve number of all Python packages in Thoth Database.""" with self._session_scope() as session: query = session.query(PythonPackageVersionEntity) if distinct: query = query.distinct() return query.count()
[docs] def get_python_package_version_entities_names_all( self, ) -> List[str]: """Retrieve names of Python package entities in the Thoth's knowledge base.""" with self._session_scope() as session: query = session.query(PythonPackageVersionEntity.package_name) return [i[0] for i in query.distinct().all()]
[docs] def get_python_package_version_names_all( self, *, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, distinct: bool = False, ) -> List[str]: """Retrieve names of Python Packages known by Thoth. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_python_packages_names_all() ['regex', 'tensorflow'] """ os_name = map_os_name(os_name) os_version = normalize_os_version(os_name, os_version) with self._session_scope() as session: query = session.query(PythonPackageVersion).with_entities(PythonPackageVersion.package_name) if os_name is not None: query = query.filter(PythonPackageVersion.os_name == os_name) if os_version is not None: query = query.filter(PythonPackageVersion.os_version == os_version) if python_version is not None: query = query.filter(PythonPackageVersion.python_version == python_version) if distinct: query = query.distinct() result = query.all() return [item[0] for item in result]
[docs] def get_python_packages_all( self, *, start_offset: int = 0, count: Optional[int] = DEFAULT_COUNT, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, distinct: bool = False, ) -> List[Tuple[str, str]]: """Retrieve Python packages with index in Thoth Database. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_python_packages_all() [('regex', 'https://pypi.org/simple'), ('tensorflow', 'https://pypi.org/simple')] """ os_name = map_os_name(os_name) os_version = normalize_os_version(os_name, os_version) with self._session_scope() as session: query = ( session.query(PythonPackageVersion) .join(PythonPackageIndex) .with_entities(PythonPackageVersion.package_name, PythonPackageIndex.url) ) if os_name is not None: query = query.filter(PythonPackageVersion.os_name == os_name) if os_version is not None: query = query.filter(PythonPackageVersion.os_version == os_version) if python_version is not None: query = query.filter(PythonPackageVersion.python_version == python_version) query = query.offset(start_offset).limit(count) if distinct: query = query.distinct() return query.all()
@staticmethod def _construct_python_packages_query( session: Session, *, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, ) -> Query: """Construct query for Python packages functions, the query is not executed.""" query = ( session.query(PythonPackageVersion) .join(PythonPackageIndex) .group_by(PythonPackageVersion.package_name, PythonPackageVersion.package_version, PythonPackageIndex.url) .with_entities( PythonPackageVersion.package_name, PythonPackageVersion.package_version, PythonPackageIndex.url ) ) if os_name is not None: query = query.filter(PythonPackageVersion.os_name == os_name) if os_version is not None: query = query.filter(PythonPackageVersion.os_version == os_version) if python_version is not None: query = query.filter(PythonPackageVersion.python_version == python_version) return query
[docs] def get_python_packages_count_all( self, *, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, distinct: bool = False, ) -> int: """Retrieve number of versions per Python package in Thoth Database.""" with self._session_scope() as session: query = self._construct_python_packages_query( session, os_name=os_name, os_version=os_version, python_version=python_version ) if distinct: query = query.distinct() return query.count()
[docs] def get_python_packages_all_versions( self, *, start_offset: int = 0, count: Optional[int] = DEFAULT_COUNT, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, distinct: bool = False, ) -> Dict[str, List[Tuple[str, str]]]: """Retrieve Python package versions per package in Thoth Database. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_python_packages_all_versions() {'absl-py': [('0.1.10', 'https://pypi.org/simple'), ('0.2.1', 'https://pypi.org/simple')]} """ os_name = map_os_name(os_name) os_version = normalize_os_version(os_name, os_version) with self._session_scope() as session: query = self._construct_python_packages_query( session, os_name=os_name, os_version=os_version, python_version=python_version ) query = query.offset(start_offset).limit(count) if distinct: query = query.distinct() query_result = query.all() return self._group_by_package_name(result=query_result)
[docs] def get_python_package_versions_count( self, *, start_offset: int = 0, count: Optional[int] = DEFAULT_COUNT, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, distinct: bool = False, ) -> Dict[Tuple[str, str, str], int]: """Retrieve number of Python Package (package_name, package_version, index_url) in Thoth Database. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_python_package_versions_count() {('absl-py', '0.1.10', 'https://pypi.org/simple'): 1, ('absl-py', '0.2.1', 'https://pypi.org/simple'): 1} """ os_name = map_os_name(os_name) os_version = normalize_os_version(os_name, os_version) with self._session_scope() as session: query = ( session.query(PythonPackageVersion) .join(PythonPackageIndex) .group_by( PythonPackageVersion.package_name, PythonPackageVersion.package_version, PythonPackageIndex.url ) .with_entities( PythonPackageVersion.package_name, PythonPackageVersion.package_version, PythonPackageIndex.url, func.count( tuple_( PythonPackageVersion.package_name, PythonPackageVersion.package_version, PythonPackageIndex.url, ) ), ) ) if os_name is not None: query = query.filter(PythonPackageVersion.os_name == os_name) if os_version is not None: query = query.filter(PythonPackageVersion.os_version == os_version) if python_version is not None: query = query.filter(PythonPackageVersion.python_version == python_version) query = query.offset(start_offset).limit(count) if distinct: query = query.distinct() result = query.all() return self._count_per_package(result=result)
[docs] def get_python_package_versions_all_count( self, *, start_offset: int = 0, count: Optional[int] = DEFAULT_COUNT, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, distinct: bool = False, sort_by: QuerySortTypeEnum = None, ) -> PythonQueryResult: """Retrieve number of versions per Python package name in Thoth Database. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_python_package_versions_all_count() {'setuptools': 988, 'pip': 211, 'termcolor': 14, 'six': 42} """ os_name = map_os_name(os_name) os_version = normalize_os_version(os_name, os_version) with self._session_scope() as session: query = ( session.query(PythonPackageVersion) .join(PythonPackageIndex) .group_by(PythonPackageVersion.package_name) .with_entities(PythonPackageVersion.package_name, func.count(PythonPackageVersion.package_version)) ) if os_name is not None: query = query.filter(PythonPackageVersion.os_name == os_name) if os_version is not None: query = query.filter(PythonPackageVersion.os_version == os_version) if python_version is not None: query = query.filter(PythonPackageVersion.python_version == python_version) if sort_by and sort_by == QuerySortTypeEnum.PACKAGE_NAME: query = query.order_by(PythonPackageVersion.package_name) group_count = query.count() query = query.offset(start_offset).limit(count) if distinct: query = query.distinct() result = query.all() if sort_by and sort_by == QuerySortTypeEnum.PACKAGE_VERSION: raise SortTypeQueryError("To be implemented.") # TODO: To be implemented output = PythonQueryResult(result={item[0]: item[1] for item in result}, count=group_count) return output
[docs] def get_python_package_versions_count_per_index( self, index_url: str, *, start_offset: int = 0, count: Optional[int] = DEFAULT_COUNT, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, distinct: bool = False, ) -> Dict[str, Dict[Tuple[str, str], int]]: """Retrieve number of Python package versions per index url in Thoth Database. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_python_package_versions_count_per_index(index_url='https://pypi.org/simple') {'https://pypi.org/simple': {('absl-py', '0.1.10'): 1, ('absl-py', '0.2.1'): 1}} """ index_url = self.normalize_python_index_url(index_url) os_name = map_os_name(os_name) os_version = normalize_os_version(os_name, os_version) with self._session_scope() as session: query = ( session.query(PythonPackageVersion) .join(PythonPackageIndex) .filter(PythonPackageIndex.url == index_url) .with_entities( PythonPackageVersion.package_name, PythonPackageVersion.package_version, PythonPackageIndex.url, func.count(tuple_(PythonPackageVersion.package_name, PythonPackageVersion.package_version)), ) .group_by( PythonPackageVersion.package_name, PythonPackageVersion.package_version, PythonPackageIndex.url ) ) if os_name is not None: query = query.filter(PythonPackageVersion.os_name == os_name) if os_version is not None: query = query.filter(PythonPackageVersion.os_version == os_version) if python_version is not None: query = query.filter(PythonPackageVersion.python_version == python_version) query = query.offset(start_offset).limit(count) if distinct: query = query.distinct() result = query.all() return self._count_per_index(result=result, index_url=index_url)
[docs] def get_python_package_versions_count_per_version( self, package_name: str, *, start_offset: int = 0, count: Optional[int] = DEFAULT_COUNT, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, distinct: bool = False, ) -> Dict[str, Dict[str, int]]: """Retrieve number of Python package versions per index url in Thoth Database. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_python_package_versions_count_per_version(package_name='tensorflow') {'1.14.0rc0': {'https://pypi.org/simple': 1}, '1.13.0rc2': {'https://pypi.org/simple': 1}} """ package_name = self.normalize_python_package_name(package_name) os_name = map_os_name(os_name) os_version = normalize_os_version(os_name, os_version) with self._session_scope() as session: query = ( session.query(PythonPackageVersion) .join(PythonPackageIndex) .filter(PythonPackageVersion.package_name == package_name) .with_entities( PythonPackageVersion.package_name, PythonPackageVersion.package_version, PythonPackageIndex.url, func.count( tuple_( PythonPackageVersion.package_name, PythonPackageVersion.package_version, PythonPackageIndex.url, ) ), ) .group_by( PythonPackageVersion.package_name, PythonPackageVersion.package_version, PythonPackageIndex.url ) ) if os_name is not None: query = query.filter(PythonPackageVersion.os_name == os_name) if os_version is not None: query = query.filter(PythonPackageVersion.os_version == os_version) if python_version is not None: query = query.filter(PythonPackageVersion.python_version == python_version) query = query.offset(start_offset).limit(count) if distinct: query = query.distinct() result = query.all() return self._count_per_version(result=result)
def _construct_python_package_versions_query( self, session: Session, package_name: Optional[str] = None, package_version: Optional[str] = None, index_url: Optional[str] = None, *, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, is_missing: Optional[bool] = None, ) -> Query: """Construct query for Python packages versions functions, the query is not executed.""" index_url = self.normalize_python_index_url(index_url) query = ( session.query(PythonPackageVersion) .join(PythonPackageIndex) .with_entities( PythonPackageVersion.package_name, PythonPackageVersion.package_version, PythonPackageIndex.url ) ) if package_name is not None: package_name = self.normalize_python_package_name(package_name) query = query.filter(PythonPackageVersion.package_name == package_name) if package_version is not None: package_version = self.normalize_python_package_version(package_version) query = query.filter(PythonPackageVersion.package_version == package_version) if index_url is not None: query = query.filter(PythonPackageIndex.url == index_url) if os_name is not None: query = query.filter(PythonPackageVersion.os_name == os_name) if os_version is not None: query = query.filter(PythonPackageVersion.os_version == os_version) if python_version is not None: query = query.filter(PythonPackageVersion.python_version == python_version) if is_missing is not None: query = query.filter(PythonPackageVersion.is_missing == is_missing) return query
[docs] def get_python_package_versions_all( self, package_name: Optional[str] = None, package_version: Optional[str] = None, index_url: Optional[str] = None, *, start_offset: int = 0, count: Optional[int] = DEFAULT_COUNT, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, distinct: bool = False, is_missing: Optional[bool] = None, ) -> List[Tuple[str, str, str]]: """Retrieve Python package versions in Thoth Database. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_python_package_versions_all() [('regex', '2018.11.7', 'https://pypi.org/simple'), ('tensorflow', '1.11.0', 'https://pypi.org/simple')] """ index_url = self.normalize_python_index_url(index_url) os_name = map_os_name(os_name) os_version = normalize_os_version(os_name, os_version) with self._session_scope() as session: query = self._construct_python_package_versions_query( session, package_name=package_name, package_version=package_version, index_url=index_url, os_name=os_name, os_version=os_version, python_version=python_version, is_missing=is_missing, ) query = query.offset(start_offset).limit(count) if distinct: query = query.distinct() return query.all()
[docs] def get_python_package_versions_count_all( self, package_name: Optional[str] = None, package_version: Optional[str] = None, index_url: Optional[str] = None, *, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, distinct: bool = False, is_missing: Optional[bool] = None, ) -> int: """Retrieve Python package versions number in Thoth Database.""" index_url = self.normalize_python_index_url(index_url) os_name = map_os_name(os_name) os_version = normalize_os_version(os_name, os_version) with self._session_scope() as session: query = self._construct_python_package_versions_query( session, package_name=package_name, package_version=package_version, index_url=index_url, os_name=os_name, os_version=os_version, python_version=python_version, is_missing=is_missing, ) if distinct: query = query.distinct() return query.count()
def _get_multi_values_key_python_package_version_metadata( self, python_package_metadata_id: int ) -> Dict[str, Optional[List[str]]]: """Retrieve multi values key metadata for Python package metadata.""" with self._session_scope() as session: multi_value_results = {} for key, tables in self._MULTI_VALUE_KEY_PYTHON_PACKAGE_METADATA_MAP.items(): query = ( session.query(tables[0]) .filter(tables[0].python_package_metadata_id == python_package_metadata_id) .join(tables[1]) ).with_entities(tables[1]) multi_value_results[key] = [getattr(v, tables[2]) for v in query.all()] distutils_result = dict([(key, []) for key in ["requires_dist", "provides_dist", "obsolete_dist"]]) multi_value_results.update(distutils_result) d_query = ( session.query(HasMetadataDistutils) .filter(HasMetadataDistutils.python_package_metadata_id == python_package_metadata_id) .join(PythonPackageMetadataDistutils) ).with_entities(PythonPackageMetadataDistutils) for distutil in d_query.all(): distutil_dict = distutil.to_dict() if distutil_dict["distutils_type"] == MetadataDistutilsTypeEnum.REQUIRED.value: multi_value_results["requires_dist"].append(distutil_dict["distutils"]) elif distutil_dict["distutils_type"] == MetadataDistutilsTypeEnum.PROVIDED.value: multi_value_results["provides_dist"].append(distutil_dict["distutils"]) elif distutil_dict["distutils_type"] == MetadataDistutilsTypeEnum.OBSOLETE.value: multi_value_results["obsolete_dist"].append(distutil_dict["distutils"]) else: _LOGGER.warning("Distutils type not registered in Thoth.") return multi_value_results
[docs] def get_python_package_version_metadata( self, package_name: str, package_version: str, index_url: str ) -> Dict[str, str]: """Retrieve Python package metadata.""" index_url = self.normalize_python_index_url(index_url) package_name = self.normalize_python_package_name(package_name) package_version = self.normalize_python_package_version(package_version) with self._session_scope() as session: query = ( session.query(PythonPackageVersion) .filter( and_( PythonPackageVersion.package_name == package_name, PythonPackageVersion.package_version == package_version, PythonPackageVersion.python_package_metadata_id.isnot(None), ) ) .join(PythonPackageIndex) .filter(PythonPackageIndex.url == index_url) .join(PythonPackageMetadata) ).with_entities(PythonPackageMetadata) result = query.first() if result is None: raise NotFoundError(f"No record found for {package_name!r}, {package_version!r}, {index_url!r}") formatted_result = result.to_dict() formatted_result.update(self._get_multi_values_key_python_package_version_metadata(result.id)) return formatted_result
[docs] def get_unsolved_python_packages_all_per_adviser_run(self, source_type: str) -> Dict[str, List[str]]: """Retrieve all unsolved packages for a certain Adviser Run that need to be re run. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_unsolved_python_packages_all_per_adviser_run() {'adviser-04ab56d6': ['black'], 'adviser-054ab56d6': ['black', 'numpy']} """ with self._session_scope() as session: query = ( session.query(AdviserRun) .filter(AdviserRun.need_re_run.is_(True)) .filter(AdviserRun.source_type == source_type) .filter(AdviserRun.re_run_adviser_id.is_(None)) .join(HasUnresolved) .join(PythonPackageVersionEntity) ).with_entities(AdviserRun.adviser_document_id, PythonPackageVersionEntity.package_name) query_result = query.all() result = {} for couple in query_result: result.setdefault(couple[0], []).append(couple[1]) return result
def _create_python_package_requirement( self, session: Session, requirements: dict ) -> List[PythonPackageRequirement]: """Create requirements for un-pinned Python packages.""" result = [] pipfile = Pipfile.from_dict(requirements) for requirement in pipfile.packages.packages.values(): index = None if requirement.index is not None: index = self._get_or_create_python_package_index(session, requirement.index.url, only_if_enabled=False) python_package_requirement, _ = PythonPackageRequirement.get_or_create( session, name=self.normalize_python_package_name(requirement.name), version_range=requirement.version, python_package_index_id=index.id if index else None, develop=requirement.develop, ) result.append(python_package_requirement) return result def _create_python_packages_pipfile( self, session: Session, pipfile_locked: dict, software_environment: SoftwareEnvironment = None, sync_only_entity: bool = False, ) -> List[PythonPackageVersion]: """Create Python packages from Pipfile.lock entries and return them.""" result = [] pipfile_locked = PipfileLock.from_dict(pipfile_locked, pipfile=None) os_name = software_environment.os_name if software_environment else None os_version = software_environment.os_version if software_environment else None python_version = software_environment.python_version if software_environment else None if sync_only_entity: for package in pipfile_locked.packages.packages.values(): result.append( self._create_python_package_version( session, package_name=package.name, package_version=package.locked_version, os_name=os_name, os_version=os_version, python_version=python_version, index_url=package.index.url if package.index else None, sync_only_entity=sync_only_entity, ) ) return result else: for package in pipfile_locked.packages.packages.values(): # Check if the package has a known index if package.index: python_package_version = ( session.query(PythonPackageVersion) .join(PythonPackageIndex) .filter(PythonPackageVersion.package_name == package.name) .filter(PythonPackageVersion.package_version == package.locked_version) .filter(PythonPackageVersion.os_name == os_name) .filter(PythonPackageVersion.os_version == os_version) .filter(PythonPackageVersion.python_version == python_version) .filter(PythonPackageIndex.url == package.index.url if package.index else None) .first() ) else: raise PythonIndexNotProvided( f"Trying to sync package {package.name!r} in version {package.locked_version!r} " "which does not have corresponding Python entity record" ) # Check if we run the solver for a specific package already if python_package_version: result.append( self._create_python_package_version( session, package_name=package.name, package_version=package.locked_version, os_name=os_name, os_version=os_version, python_version=python_version, index_url=package.index.url if package.index else None, python_package_metadata_id=python_package_version.python_package_metadata_id, sync_only_entity=sync_only_entity, ) ) else: raise SolverNotRun( f"Trying to sync package {package.name!r} in version {package.locked_version!r} " f"not solved by solver-{os_name}-{os_version}-{python_version}" ) return result def _runtime_environment_conf2models( self, session: Session, runtime_environment: dict, environment_type: str, is_external: bool ) -> Tuple[HardwareInformation, SoftwareEnvironment]: """Create models out of runtime environment configuration.""" hardware = runtime_environment.get("hardware", {}) os = runtime_environment.get("operating_system", {}) if is_external: hardware_information_type = ExternalHardwareInformation software_environment_type = ExternalSoftwareEnvironment else: hardware_information_type = HardwareInformation software_environment_type = SoftwareEnvironment hardware_information, _ = hardware_information_type.get_or_create( session, cpu_vendor=hardware.get("cpu_vendor"), cpu_model=hardware.get("cpu_model"), cpu_cores=hardware.get("cpu_cores"), cpu_model_name=hardware.get("cpu_model_name"), cpu_family=hardware.get("cpu_family"), cpu_physical_cpus=hardware.get("cpu_physical_cpus"), gpu_model_name=hardware.get("gpu_model_name"), gpu_vendor=hardware.get("gpu_vendor"), gpu_cores=hardware.get("gpu_cores"), gpu_memory_size=hardware.get("gpu_memory_size"), ram_size=hardware.get("ram_size"), ) os_name = map_os_name(os.get("name")) software_environment, _ = software_environment_type.get_or_create( session, environment_name=runtime_environment.get("name"), python_version=runtime_environment.get("python_version"), image_name=None, image_sha=None, os_name=os_name, os_version=normalize_os_version(os_name, os.get("version")), cuda_version=runtime_environment.get("cuda_version"), environment_type=environment_type, ) return hardware_information, software_environment
[docs] def create_hardware_information(self, hardware: Dict[str, Any], is_external: bool = True) -> int: """Create hardware information in the database.""" hardware_info = dict(hardware) hardware_information_type = ExternalHardwareInformation if is_external else HardwareInformation with self._session_scope() as session: hardware_information, _ = hardware_information_type.get_or_create( session, cpu_vendor=hardware_info.pop("cpu_vendor"), cpu_model=hardware_info.pop("cpu_model"), cpu_cores=hardware_info.pop("cpu_cores"), cpu_model_name=hardware_info.pop("cpu_model_name"), cpu_family=hardware_info.pop("cpu_family"), cpu_physical_cpus=hardware_info.pop("cpu_physical_cpus"), gpu_model_name=hardware_info.pop("gpu_model_name"), gpu_vendor=hardware_info.pop("gpu_vendor"), gpu_cores=hardware_info.pop("gpu_cores"), gpu_memory_size=hardware_info.pop("gpu_memory_size"), ram_size=hardware_info.pop("ram_size"), ) hardware_information_id = hardware_information.id if hardware_info: _LOGGER.warning("Unknown parts of the hardware not synced into the database: %r", hardware_info) return hardware_information_id
[docs] def delete_hardware_information(self, hardware_information_id: int, is_external: bool = True) -> None: """Delete hardware information entry with the given id.""" hardware_information_type = ExternalHardwareInformation if is_external else HardwareInformation with self._session_scope() as session: session.query(hardware_information_type).filter( hardware_information_type.id == hardware_information_id ).delete() session.commit()
[docs] def create_github_app_installation(self, slug: str, repo_name: str, private: bool, installation_id: str) -> bool: """Create a record for new installation or reactivate uninstalled installation. Example - "installation_id": "236796147", "repo_name": "advisor", "slug": "thoth-station/advisor", "private": False Accepts installation details passed down by Github. :rtype: True, False :returns True: if installation existed and was updated :returns False: if installation was newly added. """ with self._session_scope() as session: instance = ( session.query(KebechetGithubAppInstallations) .filter(KebechetGithubAppInstallations.slug == slug) .first() ) if instance: instance.installation_id = installation_id instance.private = private instance.is_active = True session.commit() return True else: _, newly_added = KebechetGithubAppInstallations.get_or_create( session, slug=slug, repo_name=repo_name, private=private, installation_id=installation_id, is_active=True, last_run=datetime.utcnow(), ) return newly_added
[docs] def get_kebechet_github_app_installations_all( self, *, id: Optional[int] = None, slug: Optional[str] = None, private: Optional[bool] = None, installation_id: Optional[str] = None, is_active: Optional[bool] = None, runtime_environment_name: Optional[str] = None, info_manager: Optional[bool] = None, pipfile_requirements_manager: Optional[bool] = None, udpate_manager: Optional[bool] = None, version_manager: Optional[bool] = None, thoth_advise_manager: Optional[bool] = None, thoth_provenance_manager: Optional[bool] = None, last_run_before: Optional[datetime] = None, last_run_after: Optional[datetime] = None, external_python_software_stack_id: Optional[int] = None, external_software_environment_id: Optional[int] = None, advised_python_software_stack_id: Optional[int] = None, ) -> List[Dict[str, Any]]: """Get all github kebechet installations with optional filters on values Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_kebechet_github_installations_all() [ { "id": 0, "slug": "thoth-station/storages", "repo_name": "storages", "private": False, "is_active": True, "info_manager": True, "pipfile_requirements_manager": True, ... }, ... ] :rtype: List[Dict[str, Any]] :returns: A list of kebechet installations which match the applied filters """ with self._session_scope() as session: query = session.query(KebechetGithubAppInstallations) if id is not None: query = query.filter(KebechetGithubAppInstallations.id == id) if slug is not None: query = query.filter(KebechetGithubAppInstallations.slug == slug) if private is not None: query = query.filter(KebechetGithubAppInstallations.private == private) if installation_id is not None: query = query.filter(KebechetGithubAppInstallations.installation_id == installation_id) if is_active is not None: query = query.filter(KebechetGithubAppInstallations.is_active == is_active) if runtime_environment_name is not None: query = query.filter( KebechetGithubAppInstallations.runtime_environment_name == runtime_environment_name ) if info_manager is not None: query = query.filter(KebechetGithubAppInstallations.info_manager == info_manager) if pipfile_requirements_manager is not None: query = query.filter( KebechetGithubAppInstallations.pipfile_requirements_manager == pipfile_requirements_manager ) if update_manager is not None: query = query.filter(KebechetGithubAppInstallations.update_manager == update_manager) if version_manager is not None: query = query.filter(KebechetGithubAppInstallations.version_manager == version_manager) if thoth_advise_manager is not None: query = query.filter(KebechetGithubAppInstallations.thoth_advise_manager == thoth_advise_manager) if thoth_provenance_manager is not None: query = query.filter( KebechetGithubAppInstallations.thoth_provenance_manager == thoth_provenance_manager ) if last_run_before is not None: query = query.filter(KebechetGithubAppInstallations.last_run <= last_run_before) if last_run_after is not None: query = query.filter(KebechetGithubAppInstallations.last_run >= last_run_after) if external_python_software_stack_id is not None: query = query.filter( KebechetGithubAppInstallations.external_python_software_stack_id == external_python_software_stack_id ) if external_software_environment_id is not None: query = query.filter( KebechetGithubAppInstallations.external_software_environment_id == external_software_environment_id ) if advised_python_software_stack_id is not None: query = query.filter( KebechetGithubAppInstallations.advised_python_software_stack_id == advised_python_software_stack_id ) return [i.to_dict() for i in query.all()]
[docs] def delete_kebechet_github_app_installations( self, *, id: Optional[int] = None, slug: Optional[str] = None, private: Optional[bool] = None, installation_id: Optional[str] = None, is_active: Optional[bool] = None, runtime_environment_name: Optional[str] = None, info_manager: Optional[bool] = None, pipfile_requirements_manager: Optional[bool] = None, udpate_manager: Optional[bool] = None, version_manager: Optional[bool] = None, thoth_advise_manager: Optional[bool] = None, thoth_provenance_manager: Optional[bool] = None, last_run_before: Optional[datetime] = None, last_run_after: Optional[datetime] = None, external_python_software_stack_id: Optional[int] = None, external_software_environment_id: Optional[int] = None, advised_python_software_stack_id: Optional[int] = None, ) -> int: """Delete github kebechet installations which match the given filters Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.delete_kebechet_github_app_installations(slug="foo/bar", runtime_environment_name="baz") [ { "id": 0, "slug": "thoth-station/storages", "repo_name": "storages", "private": False, "is_active": True, "info_manager": True, "pipfile_requirements_manager": True, ... }, ... ] :rtype: int :returns: Number of entries which have been deleted """ with self._session_scope() as session: query = session.query(KebechetGithubAppInstallations) if id is not None: query = query.filter(KebechetGithubAppInstallations.id == id) if slug is not None: query = query.filter(KebechetGithubAppInstallations.slug == slug) if private is not None: query = query.filter(KebechetGithubAppInstallations.private == private) if installation_id is not None: query = query.filter(KebechetGithubAppInstallations.installation_id == installation_id) if is_active is not None: query = query.filter(KebechetGithubAppInstallations.is_active == is_active) if runtime_environment_name is not None: query = query.filter( KebechetGithubAppInstallations.runtime_environment_name == runtime_environment_name ) if info_manager is not None: query = query.filter(KebechetGithubAppInstallations.info_manager == info_manager) if pipfile_requirements_manager is not None: query = query.filter( KebechetGithubAppInstallations.pipfile_requirements_manager == pipfile_requirements_manager ) if update_manager is not None: query = query.filter(KebechetGithubAppInstallations.update_manager == update_manager) if version_manager is not None: query = query.filter(KebechetGithubAppInstallations.version_manager == version_manager) if thoth_advise_manager is not None: query = query.filter(KebechetGithubAppInstallations.thoth_advise_manager == thoth_advise_manager) if thoth_provenance_manager is not None: query = query.filter( KebechetGithubAppInstallations.thoth_provenance_manager == thoth_provenance_manager ) if last_run_before is not None: query = query.filter(KebechetGithubAppInstallations.last_run <= last_run_before) if last_run_after is not None: query = query.filter(KebechetGithubAppInstallations.last_run >= last_run_after) if external_python_software_stack_id is not None: query = query.filter( KebechetGithubAppInstallations.external_python_software_stack_id == external_python_software_stack_id ) if external_software_environment_id is not None: query = query.filter( KebechetGithubAppInstallations.external_software_environment_id == external_software_environment_id ) if advised_python_software_stack_id is not None: query = query.filter( KebechetGithubAppInstallations.advised_python_software_stack_id == advised_python_software_stack_id ) count = query.count() query.delete() return count
[docs] def update_kebechet_github_installations_on_is_active(self, slug: str) -> bool: """Deactivate the app on getting an uninstall event. Passed a slug name to be deactivated. Example - slug:'thoth-station/advisor' :rtype: True, False :returns True: if installation existed and was deactivated. :returns False: if installation was not found. """ with self._session_scope() as session: instances = session.query(KebechetGithubAppInstallations).filter( KebechetGithubAppInstallations.slug == slug ) if instances.all() == []: raise NotFoundError(f"No entries found for slug={slug}") instances.update({"is_active": False}, synchronize_session="fetch") session.commit() return True
[docs] def get_active_kebechet_github_installations_repos(self) -> List[str]: """Get all active repositories names with active Kebechet installation. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_active_kebechet_github_installations_repos() ['repository_foo_fullname', 'repository_bar_fullname', ...] """ with self._session_scope() as session: active_installations = ( session.query(KebechetGithubAppInstallations) .filter(KebechetGithubAppInstallations.is_active.is_(True)) .with_entities(KebechetGithubAppInstallations.slug) .all() ) return [obj[0] for obj in active_installations]
[docs] def get_active_kebechet_github_installations_repos_count_all(self) -> int: """Return the count of active repos with Kebechet installation. Example: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.connect() >>> graph.get_active_kebechet_github_installations_repos_count_all() 165 """ with self._session_scope() as session: count = ( session.query(KebechetGithubAppInstallations) .filter(KebechetGithubAppInstallations.is_active.is_(True)) .distinct(KebechetGithubAppInstallations.slug) # so we only get one entry from each installation .count() ) return count
[docs] def get_kebechet_github_installations_active_managers( self, slug: str, runtime_environment_name: Optional[str] = None ) -> list: """Return the list of active managers for a particular repository. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_kebechet_github_installations_active_managers( slug="thoth-station/srcops-testing" ) ['thoth_advise_manager'] """ with self._session_scope() as session: instance = ( session.query(KebechetGithubAppInstallations) .filter(KebechetGithubAppInstallations.is_active.is_(True)) .filter(KebechetGithubAppInstallations.slug == slug) .filter(KebechetGithubAppInstallations.runtime_environment_name == runtime_environment_name) .with_entities( KebechetGithubAppInstallations.info_manager, KebechetGithubAppInstallations.pipfile_requirements_manager, KebechetGithubAppInstallations.update_manager, KebechetGithubAppInstallations.version_manager, KebechetGithubAppInstallations.thoth_advise_manager, KebechetGithubAppInstallations.thoth_provenance_manager, ) .first() ) return [manager for manager, is_active in instance._asdict().items() if is_active == True]
[docs] def get_kebechet_github_installations_active_managers_count_all( self, kebechet_manager: str, distinct: bool = False ) -> int: """Return the number of repos with specific manager active. :rtype: int :returns Number of active records for registered Kebechet manager. """ if kebechet_manager not in KebechetManagerEnum._member_names_: raise NotFoundError( f"Manager {kebechet_manager!r} is not valid manager name. " f"Registered managers names are: {KebechetManagerEnum._member_names_!r}" ) with self._session_scope() as session: query = ( session.query(KebechetGithubAppInstallations) .filter(KebechetGithubAppInstallations.is_active.is_(True)) .distinct(KebechetGithubAppInstallations.slug) ) # we make slug distinct here so that we don't double count when the repo has multiple runtime environments if kebechet_manager == KebechetManagerEnum.INFO_MANAGER.name: query = query.filter(KebechetGithubAppInstallations.info_manager.is_(True)) if kebechet_manager == KebechetManagerEnum.PIPFILE_REQUIREMENTS_MANAGER.name: query = query.filter(KebechetGithubAppInstallations.pipfile_requirements_manager.is_(True)) if kebechet_manager == KebechetManagerEnum.UPDATE_MANAGER.name: query = query.filter(KebechetGithubAppInstallations.update_manager.is_(True)) if kebechet_manager == KebechetManagerEnum.VERSION_MANAGER.name: query = query.filter(KebechetGithubAppInstallations.version_manager.is_(True)) if kebechet_manager == KebechetManagerEnum.THOTH_ADVISE_MANAGER.name: query = query.filter(KebechetGithubAppInstallations.thoth_advise_manager.is_(True)) if kebechet_manager == KebechetManagerEnum.THOTH_PROVENANCE_MANAGER.name: query = query.filter(KebechetGithubAppInstallations.thoth_provenance_manager.is_(True)) if distinct: query = query.distinct() return query.count()
[docs] def get_kebechet_github_installation_info_with_software_environment_all( self, *, python_version: Optional[str] = None, image_name: Optional[str] = None, image_sha: Optional[str] = None, os_name: Optional[str] = None, os_version: Optional[str] = None, thoth_s2i_image_name: Optional[str] = None, thoth_s2i_image_version: Optional[str] = None, env_image_name: Optional[str] = None, env_image_tag: Optional[str] = None, cuda_version: Optional[str] = None, environment_type: Optional[str] = None, ) -> List[Dict[str, Any]]: """Get all github kebechet installations with optional filters on software environment Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_kebechet_github_installation_info_with_software_environment_all() [ { "id": 0, "slug": "thoth-station/storages", "repo_name": "storages", "private": False, "is_active": True, "info_manager": True, "pipfile_requirements_manager": True, ... }, ... ] :rtype: List[Dict[str, Any]] :returns: A list of kebechet installations which match the applied filters """ with self._session_scope() as session, session.begin(subtransactions=True): query = ( session.query(KebechetGithubAppInstallations) .filter(KebechetGithubAppInstallations.is_active.is_(True)) .join(ExternalSoftwareEnvironment) ) if python_version: query = query.filter(ExternalSoftwareEnvironment.python_version == python_version) if image_name: query = query.filter(ExternalSoftwareEnvironment.image_name == image_name) if image_sha: query = query.filter(ExternalSoftwareEnvironment.image_sha == image_sha) if os_name: query = query.filter(ExternalSoftwareEnvironment.os_name == map_os_name(os_name)) if os_version: os_version = normalize_os_version(os_name, os_version) query = query.filter(ExternalSoftwareEnvironment.os_version == os_version) if thoth_s2i_image_name: query = query.filter(ExternalSoftwareEnvironment.thoth_s2i_image_name == thoth_s2i_image_name) if thoth_s2i_image_version: query = query.filter(ExternalSoftwareEnvironment.thoth_s2i_image_version == thoth_s2i_image_version) if env_image_name: query = query.filter(ExternalSoftwareEnvironment.env_image_name == env_image_name) if env_image_tag: query = query.filter(ExternalSoftwareEnvironment.cuda_version == cuda_version) if environment_type: query = query.filter(ExternalSoftwareEnvironment.environment_type == environment_type) return [i.to_dict() for i in query.all()]
[docs] def get_kebechet_github_installations_info_for_python_package_version( self, package_name: str, *, package_version: Optional[str] = None, index_url: Optional[str] = None, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, ) -> Dict[str, Dict[str, Any]]: """Return info about repo containing Python Package in the software stack. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_kebechet_github_installations_info_for_python_package_version( package_name='click' index_url="https://pypi.org/simple", ) { 'thoth-station/jupyter-nbrequirements': { 'installation_id': '193650988', 'private': False, 'package_name': 'click', 'package_version': '7.1.2', 'index_url': 'https://pypi.org/simple'} } """ package_name = self.normalize_python_package_name(package_name) os_name = map_os_name(os_name) os_version = normalize_os_version(os_name, os_version) with self._session_scope() as session, session.begin(subtransactions=True): query = ( session.query(KebechetGithubAppInstallations) .filter(KebechetGithubAppInstallations.is_active.is_(True)) .join(ExternalPythonSoftwareStack) .join(ExternalPythonRequirementsLock) .join(HasExternalPythonRequirementsLock) .join(PythonPackageVersionEntity) .filter(PythonPackageVersionEntity.package_name == package_name) ) if index_url: index_url = self.normalize_python_index_url(index_url) conditions = [ PythonPackageVersionEntity.python_package_index_id == PythonPackageIndex.id, PythonPackageVersionEntity.python_package_index_id.is_(None), ] if package_version: package_version = self.normalize_python_package_version(package_version) query = query.filter(PythonPackageVersionEntity.package_version == package_version) if any(se for se in [os_name, os_version, python_version]): query = query.join(ExternalSoftwareEnvironment) if os_name: query = query.filter(ExternalSoftwareEnvironment.os_name == os_name) if os_version: query = query.filter(ExternalSoftwareEnvironment.os_version == os_version) if python_version: query = query.filter(ExternalSoftwareEnvironment.python_version == python_version) if index_url: query = query.filter(exists().where(or_(*conditions))) query = query.with_entities( KebechetGithubAppInstallations.slug, KebechetGithubAppInstallations.installation_id, KebechetGithubAppInstallations.private, PythonPackageVersionEntity.package_name, PythonPackageVersionEntity.package_version, PythonPackageVersionEntity.python_package_index_id, ) result = query.all() return self._group_by_slug(result)
[docs] def update_kebechet_installation_using_files( self, slug: str, installation_id: str, requirements: Optional[dict] = None, requirements_lock: Optional[dict] = None, thoth_config: Optional[dict] = None, runtime_environment_name: Optional[str] = None, private: bool = False, ): """Update info about kebechet installation.""" with self._session_scope() as session, session.begin(subtransactions=True): if "runtime_environments" in thoth_config: if runtime_environment_name is None: env_dict = thoth_config["runtime_environments"][0] else: for env in thoth_config["runtime_environments"]: if env["name"] == runtime_environment_name: env_dict = env else: raise ValueError(f"No environment {runtime_environment_name} found in thoth configuration") os_name = map_os_name(env_dict["operating_system"]["name"]) os_version = env_dict["operating_system"]["version"] software_env = ExternalSoftwareEnvironment.get_or_create( session=session, environment_name=env_dict["name"], os_name=os_name, os_version=normalize_os_version(os_name, os_version), python_version=env_dict.get("python_version"), cuda_version=env_dict.get("cuda_version"), environment_type=EnvironmentTypeEnum.RUNTIME.value, )[0] else: software_env = None python_stack = self._create_python_software_stack( session=session, requirements=requirements, requirements_lock=requirements_lock, software_environment=software_env, is_external=True, ) manager_info = thoth_config.get("managers") or {} all_managers = [i["name"] for i in manager_info] item = ( session.query(KebechetGithubAppInstallations) .filter(KebechetGithubAppInstallations.slug == slug) .filter(KebechetGithubAppInstallations.runtime_environment_name == runtime_environment_name) .first() ) if item is None: KebechetGithubAppInstallations.get_or_create( session=session, slug=slug, repo_name=slug.split("/")[1], installation_id=installation_id, private=private, is_active=True, runtime_environment_name=runtime_environment_name, external_python_software_stack_id=python_stack.id, external_software_environment_id=software_env.id, info_manager="info" in all_managers, pipfile_requirements_manager="pipfile-requirements" in all_managers, update_manager="update" in all_managers, version_manager="version" in all_managers, thoth_advise_manager="thoth-advise" in all_managers, thoth_provenance_manager="thoth-provenance" in all_managers, ) else: session.query(KebechetGithubAppInstallations).filter( KebechetGithubAppInstallations.id == item.id ).update( { "slug": slug, "repo_name": slug.split("/")[1], "installation_id": installation_id, "private": private, "is_active": True, "runtime_environment_name": runtime_environment_name, "external_python_software_stack_id": python_stack.id, "external_software_environment_id": software_env.id, "info_manager": "info" in all_managers, "pipfile_requirements_manager": "pipfile-requirements" in all_managers, "update_manager": "update" in all_managers, "version_manager": "version" in all_managers, "thoth_advise_manager": "thoth-advise" in all_managers, "thoth_provenance_manager": "thoth-provenance" in all_managers, } )
[docs] def get_index_url_from_id(self, package_index_id: int) -> str: """Return index URL from id.""" with self._session_scope() as session: output = ( session.query(PythonPackageIndex) .filter(PythonPackageIndex.id == package_index_id) .with_entities(PythonPackageIndex.url) .first() ) return output[0]
def _group_by_slug( self, result: Union[List, Dict[str, Any]], ) -> Dict[str, List[Tuple[str, str]]]: """Format Query result to group by package name.""" query_result = {} for item in result: if item[5]: index_url = self.get_index_url_from_id(item[5]) else: index_url = item[5] query_result[item[0]] = { "installation_id": item[1], "private": item[2], "package_name": item[3], "package_version": item[4], "index_url": index_url, } return query_result
[docs] def create_python_package_version_entity( self, package_name: str, package_version: Optional[str] = None, index_url: Optional[str] = None, *, only_if_package_seen: bool = False, ) -> Optional[Tuple[PythonPackageVersionEntity, bool]]: """Create a Python package version entity record in the system. By creating this entity, the system will record and track the given package. """ index_url = self.normalize_python_index_url(index_url) package_name = self.normalize_python_package_name(package_name) if package_version is not None: package_version = self.normalize_python_package_version(package_version) with self._session_scope() as session: if only_if_package_seen: seen_count = ( session.query(PythonPackageVersionEntity) .filter(PythonPackageVersionEntity.package_name == package_name) .count() ) if seen_count == 0: return None index = None if index_url: index = self._get_or_create_python_package_index(session, index_url, only_if_enabled=False) entity, existed = PythonPackageVersionEntity.get_or_create( session, package_name=package_name, package_version=package_version, python_package_index_id=index.id if index else None, ) self._refresh_rules_python_entity(session, entity) return entity, existed
def _delete_python_package_version( self, *, package_name: str, package_version: str, index_url: str, os_name: str, os_version: str, python_version: str, ) -> int: """Delete the given package-version entry.""" # We use join so raw delete() cannot be used. deleted_count = 0 with self._session_scope() as session: for pv_id in ( session.query(PythonPackageVersion) .join(PythonPackageIndex) .filter( PythonPackageVersion.package_name == package_name, PythonPackageVersion.package_version == package_version, PythonPackageVersion.os_name == os_name, PythonPackageVersion.os_version == os_version, PythonPackageVersion.python_version == python_version, PythonPackageIndex.url == index_url, ) .with_entities(PythonPackageVersion.id) .all() ): session.query(PythonPackageVersion).filter(PythonPackageVersion.id == pv_id).delete() deleted_count += 1 return deleted_count def _create_python_package_version( self, session: Session, package_name: str, package_version: Union[str, None], index_url: Union[str, None], *, os_name: Union[str, None], os_version: Union[str, None], python_version: Union[str, None], python_package_metadata_id: int = None, sync_only_entity: bool = False, ) -> Union[PythonPackageVersion, PythonPackageVersionEntity]: """Create a Python package version. Make sure it is properly mirrored with a Python package entity and connected to a Python package index. """ package_name = self.normalize_python_package_name(package_name) if package_version is not None: package_version = self.normalize_python_package_version(package_version) index = None if index_url is not None: index_url = self.normalize_python_index_url(index_url) index = self._get_or_create_python_package_index(session, index_url, only_if_enabled=False) entity, _ = PythonPackageVersionEntity.get_or_create( session, package_name=package_name, package_version=package_version, python_package_index_id=index.id if index else None, ) self._refresh_rules_python_entity(session, entity) if sync_only_entity: return entity python_package_version, _ = PythonPackageVersion.get_or_create( session, package_name=package_name, package_version=package_version, python_package_index_id=index.id if index else None, os_name=os_name, os_version=os_version, python_version=python_version, entity_id=entity.id, python_package_metadata_id=python_package_metadata_id, ) return python_package_version @staticmethod def _create_fuzzy_hash(sorted_ids: List[int]) -> str: """Create fuzzy hash from sorted list of integers. Reference: https://pypi.org/project/python-ssdeep/ Reference: https://docs.python.org/3/library/stdtypes.html#int.to_bytes """ hash_ = "" for object_id in sorted_ids: # length of bytes required for the integer length = (object_id.bit_length() + 7) // 8 # no negative ids are passed hash_ += ssdeep.hash(object_id.to_bytes(length=length, byteorder="big")) return hash_ def _create_python_software_stack( self, session: Session, software_stack_type: Optional[str] = None, requirements: dict = None, requirements_lock: dict = None, software_environment: SoftwareEnvironment = None, *, performance_score: float = None, overall_score: float = None, is_external: bool = False, ) -> PythonSoftwareStack: """Create a Python software stack out of its JSON/dict representation.""" if requirements is not None: python_package_requirements = self._create_python_package_requirement(session, requirements) # Create unique hash for requirements to go into PythonRequirements requirements_ids = [int(ppr.id) for ppr in python_package_requirements] requirements_ids.sort() requirements_hash = self._create_fuzzy_hash(requirements_ids) if is_external: python_requirements, _ = ExternalPythonRequirements.get_or_create( session, requirements_hash=requirements_hash, ) for python_requirement in python_package_requirements: HasExternalPythonRequirements.get_or_create( session, external_python_requirements_id=python_requirements.id, python_package_requirement_id=python_requirement.id, ) else: python_requirements, _ = PythonRequirements.get_or_create( session, requirements_hash=requirements_hash, ) for python_requirement in python_package_requirements: HasPythonRequirements.get_or_create( session, python_requirements_id=python_requirements.id, python_package_requirement_id=python_requirement.id, ) if requirements_lock is not None: python_package_versions = self._create_python_packages_pipfile( session, requirements_lock, software_environment=software_environment, sync_only_entity=is_external ) # Create unique hash for requirements locked to go to PythonRequirementsLock requirements_lock_ids = [int(ppv.id) for ppv in python_package_versions] requirements_lock_ids.sort() requirements_lock_hash = self._create_fuzzy_hash(requirements_lock_ids) if is_external: external_python_requirements_lock, _ = ExternalPythonRequirementsLock.get_or_create( session, requirements_lock_hash=requirements_lock_hash, ) for python_package_version_entity in python_package_versions: HasExternalPythonRequirementsLock.get_or_create( session, external_python_requirements_locked_id=external_python_requirements_lock.id, python_package_version_entity_id=python_package_version_entity.id, ) else: python_requirements_lock, _ = PythonRequirementsLock.get_or_create( session, requirements_lock_hash=requirements_lock_hash, ) for python_package_version in python_package_versions: HasPythonRequirementsLock.get_or_create( session, python_requirements_lock_id=python_requirements_lock.id, python_package_version_id=python_package_version.id, ) if is_external: # User can submit software stack with only Pipfile if requirements_lock is None: external_python_requirements_lock, _ = ExternalPythonRequirementsLock.get_or_create( session, requirements_lock_hash=self._create_fuzzy_hash([0]), ) software_stack, _ = ExternalPythonSoftwareStack.get_or_create( session, external_python_requirements_id=python_requirements.id, external_python_requirements_lock_id=external_python_requirements_lock.id, ) else: software_stack, _ = ExternalPythonSoftwareStack.get_or_create( session, external_python_requirements_id=python_requirements.id, external_python_requirements_lock_id=external_python_requirements_lock.id, ) else: software_stack, _ = PythonSoftwareStack.get_or_create( session, performance_score=performance_score, overall_score=overall_score, software_stack_type=software_stack_type, python_requirements_id=python_requirements.id, python_requirements_lock_id=python_requirements_lock.id, ) return software_stack
[docs] def get_python_software_stack_count_all( self, is_external: bool = False, software_stack_type: Optional[str] = None, distinct: bool = False ) -> int: """Get number of Python software stacks available filtered by type.""" with self._session_scope() as session: if is_external: query = session.query(ExternalPythonSoftwareStack) else: query = session.query(PythonSoftwareStack.software_stack_type).filter( PythonSoftwareStack.software_stack_type == software_stack_type ) if distinct: return query.distinct().count() return query.count()
[docs] def sync_inspection_result(self, document) -> None: """Sync the given inspection document into the graph database.""" # Check if we have such performance model before creating any other records. inspection_document_id = document["document_id"] inspection_result_number = document["result_number"] inspection_specification = document["specification"] inspection_result = document["result"] with self._session_scope() as session, session.begin(subtransactions=True): build_cpu = OpenShift.parse_cpu_spec(inspection_specification["build"]["requests"]["cpu"]) build_memory = OpenShift.parse_memory_spec(inspection_specification["build"]["requests"]["memory"]) run_cpu = OpenShift.parse_cpu_spec(inspection_specification["run"]["requests"]["cpu"]) run_memory = OpenShift.parse_memory_spec(inspection_specification["run"]["requests"]["memory"]) # Convert bytes to GiB, we need float number given the fixed int size. run_memory = run_memory / (1024 ** 3) build_memory = build_memory / (1024 ** 3) runtime_environment = inspection_result["runtime_environment"] run_hardware_information, run_software_environment = self._runtime_environment_conf2models( session, runtime_environment, environment_type=EnvironmentTypeEnum.RUNTIME.value, is_external=False ) runtime_environment["hardware"] = inspection_specification["build"]["requests"]["hardware"] build_hardware_information, build_software_environment = self._runtime_environment_conf2models( session, runtime_environment, environment_type=EnvironmentTypeEnum.BUILDTIME.value, is_external=False ) software_stack = None if "python" in inspection_specification: # Inspection stack. software_stack = self._create_python_software_stack( session, software_stack_type=SoftwareStackTypeEnum.INSPECTION.value, requirements=inspection_specification["python"].get("requirements"), requirements_lock=inspection_specification["python"].get("requirements_locked"), software_environment=run_software_environment, performance_score=None, overall_score=None, ) inspection_run = ( session.query(InspectionRun) .filter(InspectionRun.inspection_document_id == inspection_document_id) .filter(InspectionRun.inspection_result_number == inspection_result_number) .first() ) if inspection_run and inspection_run.dependency_monkey_run_id: # Inspection was run through Dependency Monkey # INSERT…ON CONFLICT (Upsert) # https://docs.sqlalchemy.org/en/13/dialects/postgresql.html?highlight=conflict#insert-on-conflict-upsert # https://docs.sqlalchemy.org/en/13/errors.html#sql-expression-language compile required insert_stmt = insert(InspectionRun).values( id=inspection_run.dependency_monkey_run_id, inspection_document_id=inspection_document_id, inspection_result_number=inspection_result_number, dependency_monkey_run_id=inspection_run.dependency_monkey_run_id, inspection_sync_state=InspectionSyncStateEnum.PENDING.value, ) do_update_stmt = insert_stmt.on_conflict_do_update( index_elements=["id"], set_=dict( inspection_sync_state=InspectionSyncStateEnum.SYNCED.value, inspection_document_id=inspection_document_id, inspection_result_number=inspection_result_number, datetime=inspection_specification.get("@created"), amun_version=None, # TODO: propagate Amun version here which should match API version build_requests_cpu=build_cpu, build_requests_memory=build_memory, run_requests_cpu=run_cpu, run_requests_memory=run_memory, build_software_environment_id=build_software_environment.id, build_hardware_information_id=build_hardware_information.id, run_software_environment_id=run_software_environment.id, run_hardware_information_id=run_hardware_information.id, inspection_software_stack_id=software_stack.id if software_stack else None, ), ) session.execute(do_update_stmt) else: inspection_run, _ = InspectionRun.get_or_create( session, inspection_sync_state=InspectionSyncStateEnum.SYNCED.value, inspection_document_id=inspection_document_id, inspection_result_number=inspection_result_number, datetime=inspection_specification.get("@created"), amun_version=None, # TODO: propagate Amun version here which should match API version build_requests_cpu=build_cpu, build_requests_memory=build_memory, run_requests_cpu=run_cpu, run_requests_memory=run_memory, build_software_environment_id=build_software_environment.id, build_hardware_information_id=build_hardware_information.id, run_software_environment_id=run_software_environment.id, run_hardware_information_id=run_hardware_information.id, inspection_software_stack_id=software_stack.id if software_stack else None, ) if inspection_specification.get("script"): # We have run an inspection job. if not inspection_result["stdout"]: raise ValueError("No values provided for inspection output %r", inspection_document_id) performance_indicator_name = inspection_result.get("name") performance_model_class = PERFORMANCE_MODEL_BY_NAME.get(performance_indicator_name) if not performance_model_class: raise PerformanceIndicatorNotRegistered( f"No performance indicator registered for name {performance_indicator_name!r}" ) performance_indicator, _ = performance_model_class.create_from_report( session, inspection_specification=inspection_specification, inspection_result=inspection_result, inspection_run_id=inspection_run.id, )
[docs] def create_python_cve_record( self, package_name: str, package_version: str, index_url: str, *, cve_id: str, details: str, link: Optional[str], ) -> bool: """Store information about a CVE in the graph database for the given Python package.""" package_name = self.normalize_python_package_name(package_name) package_version = self.normalize_python_package_version(package_version) index_url = self.normalize_python_index_url(index_url) with self._session_scope() as session: cve = session.query(CVE).filter(CVE.cve_id == cve_id).first() if not cve: cve, _ = CVE.get_or_create( session, cve_id=cve_id, details=details, aggregated_at=datetime.utcnow(), link=link, ) index = self._get_or_create_python_package_index(session, index_url, only_if_enabled=False) entity, e = PythonPackageVersionEntity.get_or_create( session, package_name=package_name, package_version=package_version, python_package_index_id=index.id, ) self._refresh_rules_python_entity(session, entity) _, existed = HasVulnerability.get_or_create( session, cve_id=cve.id, python_package_version_entity_id=entity.id ) return existed
[docs] def set_cve_timestamp(self, timestamp: datetime) -> None: """Set CVE timestamp record.""" with self._session_scope() as session: instance = session.query(CVETimestamp).first() if instance: instance.timestamp = timestamp else: instance = CVETimestamp(timestamp=timestamp) session.add(instance) session.commit()
[docs] def get_cve_timestamp(self) -> Optional[datetime]: """Get CVE timestamp record.""" with self._session_scope() as session: query_result = session.query(CVETimestamp).with_entities(CVETimestamp.timestamp).all() if not query_result or not query_result[0]: return None if len(query_result) > 1: _LOGGER.error("Inconsistent CVE timestamp found in the database: %r", query_result) return query_result[0][0] if query_result and query_result[0] else None
[docs] def update_missing_flag_package_version( self, package_name: str, package_version: str, index_url: str, value: bool ) -> None: """Update value of is_missing flag for PythonPackageVersion.""" index_url = self.normalize_python_index_url(index_url) with self._session_scope() as session: subq = ( session.query(PythonPackageVersion) .join(PythonPackageIndex) .filter(PythonPackageVersion.package_name == package_name) .filter(PythonPackageVersion.package_version == package_version) .filter(PythonPackageIndex.url == index_url) .with_entities(PythonPackageVersion.id) ) ( session.query(PythonPackageVersion) .filter(PythonPackageVersion.id.in_(subq)) .update({"is_missing": value}, synchronize_session="fetch") )
[docs] def update_provides_source_distro_package_version( self, package_name: str, package_version: str, index_url: str, value: bool ) -> None: """Update value of is_si_analyzable flag for PythonPackageVersion.""" index_url = self.normalize_python_index_url(index_url) with self._session_scope() as session: subq = ( session.query(PythonPackageVersion) .join(PythonPackageIndex) .filter(PythonPackageVersion.package_name == package_name) .filter(PythonPackageVersion.package_version == package_version) .filter(PythonPackageIndex.url == index_url) .with_entities(PythonPackageVersion.id) ) ( session.query(PythonPackageVersion) .filter(PythonPackageVersion.id.in_(subq)) .update({"provides_source_distro": value}, synchronize_session="fetch") )
[docs] def is_python_package_version_is_missing(self, package_name: str, package_version: str, index_url: str) -> bool: """Check whether is_missing flag is set for python package version.""" index_url = self.normalize_python_index_url(index_url) with self._session_scope as session: query = ( session.query(PythonPackageVersion) .join(PythonPackageIndex) .filter(PythonPackageVersion.package_name == package_name) .filter(PythonPackageVersion.package_version == package_version) .filter(PythonPackageIndex.url == index_url) .with_entities(PythonPackageVersion.is_missing) ) if query.first() is None: raise NotFoundError( f"The given package {package_name!r} in version {package_version!r} " f"from {index_url!r} was not found" ) return query.first()[0]
[docs] def get_adviser_run_origins_all( self, package_name: Optional[str] = None, package_version: Optional[str] = None, index_url: Optional[str] = None, start_offset: int = 0, count: Optional[int] = DEFAULT_COUNT, distinct: bool = False, ) -> List[str]: """Retrieve all origins (git repos URLs) in Adviser Run. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_adviser_run_origins_all() ['https://github.com/thoth-station/storages', 'https://github.com/thoth-station/user-api', 'https://github.com/thoth-station/adviser'] """ index_url = self.normalize_python_index_url(index_url) with self._session_scope() as session: query = session.query(AdviserRun).order_by(AdviserRun.origin).order_by(AdviserRun.datetime.desc()) if package_name or package_version: query = query.join( ExternalPythonRequirementsLock, ExternalPythonRequirementsLock.python_software_stack_id == AdviserRun.user_software_stack_id, ).join( PythonPackageVersion, ExternalPythonRequirementsLock.python_package_version_entity_id == PythonPackageVersion.id, ) if index_url is not None: query = query.join(PythonPackageIndex) query = query.filter(PythonPackageIndex.url == index_url) if package_name is not None: package_name = self.normalize_python_package_name(package_name) query = query.filter(PythonPackageVersion.package_name == package_name) if package_version is not None: package_version = self.normalize_python_package_version(package_version) query = query.filter(PythonPackageVersion.package_version == package_version) query = query.offset(start_offset).limit(count) query = query.with_entities(AdviserRun.origin) if distinct: query = query.distinct() result = [r[0] for r in query.all() if r[0]] # We do not consider None results return result
@staticmethod def _filter_source_type(results: List[any]) -> Dict[str, int]: """Filter results per source type.""" return { source_result[0]: source_result[1] for source_result in results if source_result[0] in ThothAdviserIntegrationEnum._member_names_ }
[docs] def get_adviser_run_count_per_source_type( self, ) -> Dict[str, int]: """Retrieve number of Adviser run per source type in Thoth Database. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_adviser_run_count_per_source_type() {'GITHUB_APP': 154, 'CLI': 71} """ with self._session_scope() as session: query = session.query(AdviserRun.source_type, func.count(AdviserRun.source_type)).group_by( AdviserRun.source_type ) results = query.all() return self._filter_source_type(results=results)
@staticmethod def _create_date_filter(date_: str) -> datetime: """Create date filter. @params date_: DD-MM-YY """ return datetime.strptime(date_, "%d-%m-%Y").date()
[docs] def get_adviser_run_document_ids_all( self, initial_date: Optional[str] = None, final_date: Optional[str] = None, source_type: Optional[str] = None, start_offset: int = 0, count: Optional[int] = DEFAULT_COUNT, ) -> List[str]: """Retrieve adviser run document ids. @params initial_date: DD-MM-YY @params final_date: DD-MM-YY Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_adviser_run_document_ids_all() ['adviser-343231d'] """ with self._session_scope() as session: query = session.query(AdviserRun.adviser_document_id).with_entities(AdviserRun.adviser_document_id) if initial_date: date_filter = self._create_date_filter(initial_date) query = query.filter(AdviserRun.datetime > date_filter) if final_date: date_filter = self._create_date_filter(final_date) query = query.filter(AdviserRun.datetime < date_filter) if source_type: query = query.filter(AdviserRun.source_type == source_type) # query = query.offset(start_offset).limit(count) document_ids = query.all() return [obj[0] for obj in document_ids]
[docs] def get_solver_run_document_ids_all( self, initial_date: Optional[str] = None, final_date: Optional[str] = None, os_name: Optional[str] = None, os_version: Optional[str] = None, python_version: Optional[str] = None, start_offset: int = 0, count: Optional[int] = DEFAULT_COUNT, has_error: bool = False, unsolvable: bool = False, unparseable: bool = False, ) -> List[str]: """Retrieve solver run document ids. @params initial_date: DD-MM-YY @params final_date: DD-MM-YY Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_solver_run_document_ids_all() ['solver-rhel-8-py38-343231d'] """ os_name = map_os_name(os_name) os_version = normalize_os_version(os_name, os_version) with self._session_scope() as session: query = session.query(Solved.document_id).with_entities(Solved.document_id) conditions = [] if os_name or os_version or python_version: conditions.append(EcosystemSolver.id == Solved.ecosystem_solver_id) if os_name: conditions.append(EcosystemSolver.os_name == os_name) if os_version: os_version = OpenShift.normalize_os_version(os_name, os_version) conditions.append(EcosystemSolver.os_version == os_version) if python_version: conditions.append(EcosystemSolver.python_version == python_version) if has_error: query = query.filter(Solved.error.is_(True)) if unsolvable: conditions.append(Solved.error_unsolvable.is_(True)) if unparseable: conditions.append(Solved.error_unparseable.is_(True)) if conditions: query = query.filter(exists().where(and_(*conditions))) if initial_date: date_filter = self._create_date_filter(initial_date) query = query.filter(Solved.datetime > date_filter) if final_date: date_filter = self._create_date_filter(final_date) query = query.filter(Solved.datetime < date_filter) query = query.offset(start_offset).limit(count) document_ids = query.all() return [obj[0] for obj in document_ids]
[docs] def get_python_package_version_trove_classifiers_all( self, package_name: str, package_version: str, index_url: str, *, os_name: str, os_version: str, python_version: str, ) -> List[str]: """Get Python trove classifiers. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_python_package_version_trove_classifiers_all( \ "cowsay", "4.0", "https://pypi.org/simple", os_name="rhel", os_version="9", python_version="3.9") ["PROGRAMMING LANGUAGE :: PYTHON :: 3.9", "OPERATING SYSTEM :: OS INDEPENDENT"] """ self.normalize_python_package_version(package_version) self.normalize_python_package_name(package_name) self.normalize_python_index_url(index_url) with self._session_scope() as session: query = ( session.query(PythonPackageVersion) .filter( PythonPackageVersion.package_name == package_name, PythonPackageVersion.package_version == package_version, PythonPackageVersion.os_name == os_name, PythonPackageVersion.os_version == os_version, PythonPackageVersion.python_version == python_version, ) .join(PythonPackageIndex) .filter(PythonPackageIndex.url == index_url) .join(PythonPackageMetadata) .join(HasMetadataClassifier) .join(PythonPackageMetadataClassifier) .with_entities(PythonPackageMetadataClassifier.classifier) ) return [i[0] for i in query.all()]
[docs] def get_origin_count_per_source_type( self, distinct: bool = False, ) -> Dict[str, Dict[Tuple[str, str], int]]: """Retrieve number of users of adviser per source type. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_origin_count_per_source_type() {'KEBECHET': 48, 'JUPYTER_NOTEBOOK': 18, 'CLI': 513} >>> graph.get_origin_count_per_source_type(distinct=True) {'KEBECHET': 5, 'JUPYTER_NOTEBOOK': 2, 'CLI': 78} """ with self._session_scope() as session: query = session.query(AdviserRun.origin) if distinct: query = query.with_entities(AdviserRun.source_type, func.count(AdviserRun.origin.distinct())) else: query = query.with_entities(AdviserRun.source_type, func.count(AdviserRun.origin)) query = query.group_by(AdviserRun.source_type) results = query.all() return self._filter_source_type(results=results)
[docs] def update_python_package_hash_present_flag( self, package_name: str, package_version: str, index_url: str, sha256_hash: str ): """Remove hash associated with python package in the graph.""" index_url = self.normalize_python_index_url(index_url) with self._session_scope() as session: # We need to remove rows from both HasArtifact and PythonArtifact subq = ( session.query(PythonPackageVersionEntity) .filter(PythonPackageVersionEntity.package_name == package_name) .filter(PythonPackageVersionEntity.package_version == package_version) .join(PythonPackageIndex) .filter(PythonPackageIndex.url == index_url) .join(HasArtifact) .join(PythonArtifact) .filter(PythonArtifact.artifact_hash_sha256 == sha256_hash) .with_entities(PythonArtifact.id) ) # Can a hash be present on more than one python_version_entity? (session.query(PythonArtifact).filter(PythonArtifact.id.in_(subq)).update(present=False))
@staticmethod def _rpm_sync_analysis_result(session: Session, package_extract_run: PackageExtractRun, document: dict) -> None: """Sync results of RPMs found in the given container image.""" for rpm_package_info in document["result"]["rpm-dependencies"]: rpm_package_version, _ = RPMPackageVersion.get_or_create( session, package_name=rpm_package_info["name"], package_version=rpm_package_info["version"], release=rpm_package_info.get("release"), epoch=rpm_package_info.get("epoch"), arch=rpm_package_info.get("arch"), src=rpm_package_info.get("src", False), package_identifier=rpm_package_info.get("package_identifier", rpm_package_info["name"]), ) FoundRPM.get_or_create( session, package_extract_run_id=package_extract_run.id, rpm_package_version_id=rpm_package_version.id ) for dependency in rpm_package_info["dependencies"]: rpm_requirement, _ = RPMRequirement.get_or_create(session, rpm_requirement_name=dependency) RPMRequires.get_or_create( session, rpm_package_version_id=rpm_package_version.id, rpm_requirement_id=rpm_requirement.id ) @staticmethod def _deb_sync_analysis_result(session: Session, package_extract_run: PackageExtractRun, document: dict) -> None: """Sync results of deb packages found in the given container image.""" for deb_package_info in document["result"]["deb-dependencies"]: deb_package_version, _ = DebPackageVersion.get_or_create( session, package_name=deb_package_info["name"], package_version=deb_package_info["version"], epoch=deb_package_info.get("epoch"), arch=deb_package_info["arch"], ) FoundDeb.get_or_create( session, deb_package_version_id=deb_package_version.id, package_extract_run_id=package_extract_run.id ) # These three can be grouped with a zip, but that is not that readable... for pre_depends in deb_package_info.get("pre-depends") or []: deb_dependency, _ = DebDependency.get_or_create(session, package_name=pre_depends["name"]) DebPreDepends.get_or_create( session, deb_package_version_id=deb_package_version.id, deb_dependency_id=deb_dependency.id, version_range=pre_depends.get("version"), ) for depends in deb_package_info.get("depends") or []: deb_dependency, _ = DebDependency.get_or_create(session, package_name=depends["name"]) DebDepends.get_or_create( session, deb_package_version_id=deb_package_version.id, deb_dependency_id=deb_dependency.id, version_range=depends.get("version"), ) for replaces in deb_package_info.get("replaces") or []: deb_dependency, _ = DebDependency.get_or_create(session, package_name=replaces["name"]) DebReplaces.from_properties( deb_package_version_id=deb_package_version.id, deb_dependency_id=deb_dependency.id, version_range=replaces.get("version"), ) @staticmethod def _system_symbols_analysis_result( session: Session, package_extract_run: PackageExtractRun, document: dict, software_environment: Union[SoftwareEnvironment, ExternalSoftwareEnvironment], is_external: bool = False, ) -> None: """Sync system symbols detected in a package-extract run into the database.""" for library, symbols in document["result"]["system-symbols"].items(): for symbol in symbols: versioned_symbol, _ = VersionedSymbol.get_or_create(session, library_name=library, symbol=symbol) if is_external: HasSymbol.get_or_create( session, external_software_environment_id=software_environment.id, versioned_symbol_id=versioned_symbol.id, ) else: HasSymbol.get_or_create( session, software_environment_id=software_environment.id, versioned_symbol_id=versioned_symbol.id, ) DetectedSymbol.get_or_create( session, package_extract_run_id=package_extract_run.id, versioned_symbol_id=versioned_symbol.id ) def _python_sync_analysis_result( self, session: Session, package_extract_run: PackageExtractRun, document: dict, software_environment: Union[SoftwareEnvironment, ExternalSoftwareEnvironment], ) -> None: """Sync results of Python packages found in the given container image.""" for python_package_info in document["result"].get("python-packages") or []: python_package_version_entity = self._create_python_package_version( session, package_name=python_package_info["package_name"], package_version=python_package_info["package_version"], os_name=software_environment.os_name, os_version=software_environment.os_version, python_version=software_environment.python_version, index_url=None, sync_only_entity=True, ) Identified.get_or_create( session, package_extract_run_id=package_extract_run.id, python_package_version_entity_id=python_package_version_entity.id, location=python_package_info["location"], ) @staticmethod def _python_file_digests_sync_analysis_result( session: Session, package_extract_run: PackageExtractRun, document: dict ) -> None: """Sync results of Python files found in the given container image.""" for py_file in document["result"]["python-files"]: python_file_digest, _ = PythonFileDigest.get_or_create(session, sha256=py_file["sha256"]) FoundPythonFile.get_or_create( session, package_extract_run_id=package_extract_run.id, python_file_digest_id=python_file_digest.id, file=py_file["filepath"], ) @staticmethod def _python_interpreters_sync_analysis_result( session: Session, package_extract_run: PackageExtractRun, document: dict, software_environment: Union[SoftwareEnvironment, ExternalSoftwareEnvironment], ) -> None: """Sync python interpreters detected in a package-extract run into the database.""" for py_interpreter in document["result"].get("python-interpreters"): python_interpreter, _ = PythonInterpreter.get_or_create( session, path=py_interpreter.get("path"), link=py_interpreter.get("link"), version=py_interpreter.get("version"), ) FoundPythonInterpreter.get_or_create( session, python_interpreter=python_interpreter, package_extract_run=package_extract_run ) @staticmethod def _package_extract_get_env_vars(document: Dict[str, Any]) -> Dict[str, str]: """Obtain Thoth specific environment variables present in the container image.""" result = {} for entry in (document["result"].get("skopeo-inspect") or {}).get("Env") or []: if entry.startswith(("THAMOS_", "THOTH_")): env_name, env_val = entry.split("=", maxsplit=1) result[env_name] = env_val return result
[docs] def sync_analysis_result(self, document: dict) -> None: """Sync the given analysis result to the graph database.""" analysis_document_id = AnalysisResultsStore.get_document_id(document) environment_type = document["metadata"]["arguments"]["thoth-package-extract"]["metadata"]["environment_type"] environment_type = environment_type.upper() origin = document["metadata"]["arguments"]["thoth-package-extract"]["metadata"].get("origin") environment_name = document["metadata"]["arguments"]["extract-image"]["image"] os_name = map_os_name(document["result"]["operating-system"]["id"]) os_version = normalize_os_version(os_name, document["result"]["operating-system"]["version_id"]) cuda_nvcc_version = document["result"].get("cuda-version", {}).get("nvcc_version", None) cuda_found_in_file_version = document["result"].get("cuda-version", {}).get("/usr/local/cuda/version.txt", None) if ( cuda_nvcc_version is not None and cuda_found_in_file_version is not None and cuda_nvcc_version != cuda_found_in_file_version ): raise CudaVersionDoesNotMatch( f"Cuda version detected by nvcc {cuda_nvcc_version!r} is different from the one found in " f"/usr/local/cuda/version.txt " f"{document['result'].get('cuda-version', {}).get('/usr/local/cuda/version.txt', None)!r}" ) # Check if it comes from a User is_external = document["metadata"]["arguments"]["thoth-package-extract"]["metadata"].get("is_external", True) image_tag = "latest" image_name = environment_name parts = environment_name.rsplit(":", maxsplit=1) if len(parts) == 2: image_name = parts[0] image_tag = parts[1] # TODO: capture errors on image analysis? result of package-extract should be a JSON with error flag with self._session_scope() as session, session.begin(subtransactions=True): if is_external: sw_class = ExternalSoftwareEnvironment python_version = None else: sw_class = SoftwareEnvironment python_version = image_name.rsplit("-", maxsplit=1)[1] # pyXX if not re.match(r"^py\d\d$", python_version): _LOGGER.warning("No Python version information found in the the image name %r", image_name) python_version = None else: python_version = ( python_version[2:3] + "." + python_version[3:] ) # take first digit and put . after it env_vars = self._package_extract_get_env_vars(document) software_environment, _ = sw_class.get_or_create( session, environment_name=environment_name, python_version=python_version, image_name=image_name, image_sha=document["result"]["layers"][-1], os_name=os_name, os_version=os_version, thoth_s2i_image_name=env_vars.get("THOTH_S2I_NAME"), thoth_s2i_image_version=env_vars.get("THOTH_S2I_VERSION"), env_image_name=env_vars.get("IMAGE_NAME"), env_image_tag=env_vars.get("IMAGE_TAG"), cuda_version=cuda_nvcc_version or cuda_found_in_file_version, environment_type=environment_type, ) if is_external: sw_id = dict(external_software_environment_id=software_environment.id) else: sw_id = dict(software_environment_id=software_environment.id) package_extract_run, _ = PackageExtractRun.get_or_create( session, analysis_document_id=analysis_document_id, datetime=document["metadata"]["datetime"], package_extract_version=document["metadata"]["analyzer_version"], package_extract_name=document["metadata"]["analyzer"], environment_type=environment_type, origin=origin, debug=document["metadata"]["arguments"]["thoth-package-extract"]["verbose"], package_extract_error=False, image_tag=image_tag, duration=document["metadata"].get("duration"), os_id=document["result"].get("operating-system", {}).get("id"), os_name=os_name, os_version_id=os_version, image_size=document["result"].get("image_size"), **sw_id, ) self._rpm_sync_analysis_result(session, package_extract_run, document) self._deb_sync_analysis_result(session, package_extract_run, document) self._python_sync_analysis_result(session, package_extract_run, document, software_environment) self._python_file_digests_sync_analysis_result(session, package_extract_run, document) self._system_symbols_analysis_result( session, package_extract_run, document, software_environment, is_external=is_external ) self._python_interpreters_sync_analysis_result(session, package_extract_run, document, software_environment)
@staticmethod def _get_or_create_python_package_index( session: Session, index_url: str, only_if_enabled: bool = True ) -> Optional[PythonPackageIndex]: """Get or create Python package index entry with a check the given index is enabled.""" index_url = GraphDatabase.normalize_python_index_url(index_url) python_package_index = session.query(PythonPackageIndex).filter(PythonPackageIndex.url == index_url).first() if python_package_index is None: if only_if_enabled: raise PythonIndexNotRegistered(f"Python package index {index_url!r} is not know to system") python_package_index, _ = PythonPackageIndex.get_or_create(session, url=index_url) elif not python_package_index.enabled and only_if_enabled: raise PythonIndexNotRegistered(f"Python package index {index_url!r} is not enabled") return python_package_index @staticmethod def _create_multi_part_keys_metadata( session: Session, importlib_metadata: Dict[str, Any], package_metadata: PythonPackageMetadata ) -> Dict[str, Any]: """Sync multi-part keys from Python Package Metadata.""" for classifier in importlib_metadata.pop("Classifier", []): python_package_metadata_classifier, _ = PythonPackageMetadataClassifier.get_or_create( session, classifier=classifier ) HasMetadataClassifier.get_or_create( session, python_package_metadata_classifier_id=python_package_metadata_classifier.id, python_package_metadata_id=package_metadata.id, ) for platform in importlib_metadata.pop("Platform", []): python_package_metadata_platform, _ = PythonPackageMetadataPlatform.get_or_create( session, platform=platform ) HasMetadataPlatform.get_or_create( session, python_package_metadata_platform_id=python_package_metadata_platform.id, python_package_metadata_id=package_metadata.id, ) for supported_platform in importlib_metadata.pop("Supported-Platform", []): python_package_metadata_supported_platform, _ = PythonPackageMetadataSupportedPlatform.get_or_create( session, supported_platform=supported_platform ) HasMetadataSupportedPlatform.get_or_create( session, python_package_metadata_supported_platform_id=python_package_metadata_supported_platform.id, python_package_metadata_id=package_metadata.id, ) for dependency in importlib_metadata.pop("Requires-External", []): python_package_metadata_requires_external, _ = PythonPackageMetadataRequiresExternal.get_or_create( session, dependency=dependency ) HasMetadataRequiresExternal.get_or_create( session, python_package_metadata_requires_external_id=python_package_metadata_requires_external.id, python_package_metadata_id=package_metadata.id, ) for project_url in importlib_metadata.pop("Project-URL", []): python_package_metadata_project_url, _ = PythonPackageMetadataProjectUrl.get_or_create( session, project_url=project_url ) HasMetadataProjectUrl.get_or_create( session, python_package_metadata_project_url_id=python_package_metadata_project_url.id, python_package_metadata_id=package_metadata.id, ) for optional_feature in importlib_metadata.pop("Provides-Extra", []): python_package_metadata_provides_extra, _ = PythonPackageMetadataProvidesExtra.get_or_create( session, optional_feature=optional_feature ) HasMetadataProvidesExtra.get_or_create( session, python_package_metadata_provides_extra_id=python_package_metadata_provides_extra.id, python_package_metadata_id=package_metadata.id, ) for dist_key in ("Requires-Dist", "Provides-Dist", "Obsoletes-Dist"): if dist_key == "Requires-Dist": distutils_type = MetadataDistutilsTypeEnum.REQUIRED.value elif dist_key == "Provides-Dist": distutils_type = MetadataDistutilsTypeEnum.PROVIDED.value elif dist_key == "Obsoletes-Dist": distutils_type = MetadataDistutilsTypeEnum.OBSOLETE.value else: raise DistutilsKeyNotKnown(f"No distutils key registered for {dist_key!r} ") for distutils in importlib_metadata.pop(dist_key, []): python_package_metadata_distutils, _ = PythonPackageMetadataDistutils.get_or_create( session, distutils=distutils, distutils_type=distutils_type ) HasMetadataDistutils.get_or_create( session, python_package_metadata_distutils_id=python_package_metadata_distutils.id, python_package_metadata_id=package_metadata.id, ) return importlib_metadata
[docs] def sync_revsolver_result(self, document: Dict[str, Any]) -> None: """Sync results of the reverse solver. This updates relations for DependsOn on a new package release. """ dependency_name = document["metadata"]["arguments"]["app.py"]["package_name"] dependency_version = document["metadata"]["arguments"]["app.py"]["package_version"] with self._session_scope() as session, session.begin(subtransactions=True): python_package_version_entity, _ = PythonPackageVersionEntity.get_or_create( session, package_name=dependency_name, package_version=dependency_version, python_package_index_id=None ) self._refresh_rules_python_entity(session, python_package_version_entity) for entry in document["result"]: os_name = map_os_name(entry["os_name"]) os_version = entry["os_version"] python_package_version = ( session.query(PythonPackageVersion) .filter(PythonPackageVersion.package_name == entry["package_name"]) .filter(PythonPackageVersion.package_version == entry["package_version"]) .filter(PythonPackageVersion.os_name == os_name) .filter(PythonPackageVersion.os_version == normalize_os_version(os_name, os_version)) .filter(PythonPackageVersion.python_version == entry["python_version"]) .join(PythonPackageIndex) .filter(PythonPackageIndex.url == entry["index_url"]) .one() ) DependsOn.get_or_create( session, version=python_package_version, entity=python_package_version_entity, version_range=entry["version_range"], marker=entry["marker"], extra=entry["extra"], marker_evaluation_result=entry["marker_evaluation_result"], )
def _check_package_solved( self, session: Session, package_name: str, package_version: str, package_index: str ) -> Tuple: """Check if the package has been solved before syncing SI analysis to the database.""" # Check if a package have been solved by any of the solver python_package_version = ( session.query(PythonPackageVersion) .join(PythonPackageIndex) .filter(PythonPackageVersion.package_name == package_name) .filter(PythonPackageVersion.package_version == package_version) .filter(PythonPackageIndex.url == package_index) .first() ) if not python_package_version: raise SolverNotRun( f"Trying to sync package {package_name!r} in version {package_version!r} " f"not solved by any solver." ) return python_package_version.entity_id, python_package_version.id
[docs] def sync_security_indicator_aggregated_result(self, document: dict) -> None: """Sync the given security-indicator aggregated result to the graph database.""" metadata = document["metadata"] document_id = metadata["document_id"] result = document.get("result", dict()) package_name = metadata["arguments"]["app.py"]["package_name"] package_version = metadata["arguments"]["app.py"]["package_version"] index_url = metadata["arguments"]["app.py"]["package_index"] with self._session_scope() as session, session.begin(subtransactions=True): python_package_version_entity_id, python_package_version_id = self._check_package_solved( session=session, package_name=package_name, package_version=package_version, package_index=index_url ) si_aggregated_run, _ = SecurityIndicatorAggregatedRun.get_or_create( session, si_aggregated_run_document_id=document_id, datetime=metadata["datetime"], error=document.get("error", False), severity_high_confidence_high=result.get("SEVERITY.HIGH__CONFIDENCE.HIGH") or 0, severity_high_confidence_low=result.get("SEVERITY.HIGH__CONFIDENCE.LOW") or 0, severity_high_confidence_medium=result.get("SEVERITY.HIGH__CONFIDENCE.MEDIUM") or 0, severity_high_confidence_undefined=result.get("SEVERITY.HIGH__CONFIDENCE.UNDEFINED") or 0, severity_low_confidence_high=result.get("SEVERITY.LOW__CONFIDENCE.HIGH") or 0, severity_low_confidence_low=result.get("SEVERITY.LOW__CONFIDENCE.LOW") or 0, severity_low_confidence_medium=result.get("SEVERITY.LOW__CONFIDENCE.MEDIUM") or 0, severity_low_confidence_undefined=result.get("SEVERITY.LOW__CONFIDENCE.UNDEFINED") or 0, severity_medium_confidence_high=result.get("SEVERITY.MEDIUM__CONFIDENCE.HIGH") or 0, severity_medium_confidence_low=result.get("SEVERITY.MEDIUM__CONFIDENCE.LOW") or 0, severity_medium_confidence_medium=result.get("SEVERITY.MEDIUM__CONFIDENCE.MEDIUM") or 0, severity_medium_confidence_undefined=result.get("SEVERITY.MEDIUM__CONFIDENCE.UNDEFINED") or 0, number_of_analyzed_files=result["number_of_analyzed_files"], number_of_files_total=result["number_of_files_total"], number_of_files_with_severities=result["number_of_files_with_severities"], number_of_filtered_files=result["number_of_filtered_files"], number_of_python_files=result["Python.nFiles"], number_of_lines_with_comments_in_python_files=result["Python.comment"], number_of_blank_lines_in_python_files=result["Python.blank"], number_of_lines_with_code_in_python_files=result["Python.code"], total_number_of_files=result["SUM.nFiles"], total_number_of_lines=result["SUM.n_lines"], total_number_of_lines_with_comments=result["SUM.comment"], total_number_of_blank_lines=result["SUM.blank"], total_number_of_lines_with_code=result["SUM.code"], ) SIAggregated.get_or_create( session, si_aggregated_run_id=si_aggregated_run.id, python_package_version_entity_id=python_package_version_entity_id, python_package_version_id=python_package_version_id, )
[docs] def sync_solver_result(self, document: dict, *, force: bool = False) -> None: """Sync the given solver result to the graph database.""" solver_document_id = SolverResultsStore.get_document_id(document) solver_name = SolverResultsStore.get_solver_name_from_document_id(solver_document_id) solver_info = OpenShift.parse_python_solver_name(solver_name) solver_datetime = document["metadata"]["datetime"] solver_version = document["metadata"]["analyzer_version"] solver_duration = (document["metadata"].get("duration"),) os_name = solver_info["os_name"] os_version = solver_info["os_version"] python_version = solver_info["python_version"] # Older solver documents did not provide platform explictly. platform = document["result"].get("platform") or "linux-x86_64" if not self.python_package_version_depends_on_platform_exists(platform=platform): raise NotFoundError(f"No platform {platform!r} registered") with self._session_scope() as session, session.begin(subtransactions=True): ecosystem_solver, _ = EcosystemSolver.get_or_create( session, ecosystem="python", solver_name=solver_name, solver_version=solver_version, os_name=map_os_name(os_name), os_version=normalize_os_version(os_name, os_version), python_version=python_version, ) for python_package_info in document["result"]["tree"]: # Normalized in `_create_python_package_version'. package_name = python_package_info["package_name"] package_version = python_package_info["package_version_requested"] index_url = python_package_info["index_url"] importlib_metadata = python_package_info["importlib_metadata"]["metadata"] _LOGGER.info( "Syncing solver result of package %r in version %r from %r solved by %r", package_name, package_version, index_url, solver_info, ) package_metadata, _ = PythonPackageMetadata.get_or_create( session, author=importlib_metadata.pop("Author", None), author_email=importlib_metadata.pop("Author-email", None), download_url=importlib_metadata.pop("Download-URL", None), home_page=importlib_metadata.pop("Home-page", None), keywords=importlib_metadata.pop("Keywords", None), # package licence license=importlib_metadata.pop("License", None), maintainer=importlib_metadata.pop("Maintainer", None), maintainer_email=importlib_metadata.pop("Maintainer-email", None), metadata_version=importlib_metadata.pop("Metadata-Version", None), # package name name=importlib_metadata.pop("Name", None), summary=importlib_metadata.pop("Summary", None), # package version version=importlib_metadata.pop("Version", None), requires_python=importlib_metadata.pop("Requires-Python", None), description=importlib_metadata.pop("Description", None), description_content_type=importlib_metadata.pop("Description-Content-Type", None), ) # Sync Metadata keys that are arrays importlib_metadata = self._create_multi_part_keys_metadata( session, importlib_metadata=importlib_metadata, package_metadata=package_metadata ) if importlib_metadata: # There can be raised PythonPackageMetadataAttributeMissing once all metadata gathered. _LOGGER.warning( "Cannot sync the whole solver result: " f"No related columns for {list(importlib_metadata.keys())!r} " "found in PythonPackageMetadata table, the error is not fatal" ) try: python_package_version = self._create_python_package_version( session, package_name, package_version, os_name=ecosystem_solver.os_name, os_version=ecosystem_solver.os_version, python_version=ecosystem_solver.python_version, index_url=index_url, python_package_metadata_id=package_metadata.id, ) except NoResultFound: if not force: raise _LOGGER.warning( "Removing old PythonPackageVersion entry based on previous results stored and " "force parameter supplied" ) # Try to delete the given package-version and continue with the sync. self._delete_python_package_version( package_name=package_name, package_version=package_version, os_name=ecosystem_solver.os_name, os_version=ecosystem_solver.os_version, python_version=ecosystem_solver.python_version, index_url=index_url, ) python_package_version = self._create_python_package_version( session, package_name, package_version, os_name=ecosystem_solver.os_name, os_version=ecosystem_solver.os_version, python_version=ecosystem_solver.python_version, index_url=index_url, python_package_metadata_id=package_metadata.id, ) for sha256 in python_package_info["sha256"]: artifact, _ = PythonArtifact.get_or_create( session, artifact_hash_sha256=sha256, artifact_name=None # TODO: aggregate artifact names ) HasArtifact.get_or_create( session, python_artifact_id=artifact.id, python_package_version_entity_id=python_package_version.entity_id, ) solved, _ = Solved.get_or_create( session, datetime=solver_datetime, document_id=solver_document_id, version=python_package_version, ecosystem_solver=ecosystem_solver, duration=solver_duration, error=False, error_unparseable=False, error_unsolvable=False, ) # Sync imoprted package from result:tree _LOGGER.info( "Syncing imported packages for package %r in version %r from %r found by solver %r", package_name, package_version, index_url, solver_info, ) for package_call in python_package_info["packages"]: import_package, _ = ImportPackage.get_or_create( session, import_package_name=package_call, ) FoundImportPackage.get_or_create( session, python_package_version_id=python_package_version.id, import_package_id=import_package.id, ) for dependency in python_package_info["dependencies"]: for index_entry in dependency["resolved_versions"]: for dependency_version in index_entry["versions"]: dependency_entity, _ = PythonPackageVersionEntity.get_or_create( session, package_name=self.normalize_python_package_name(dependency["package_name"]), package_version=self.normalize_python_package_version(dependency_version), python_package_index_id=None, ) self._refresh_rules_python_entity(session, dependency_entity) if len(dependency.get("extra") or []) > 1: # Not sure if this can happen in the ecosystem, report error # if this incident happens. _LOGGER.error( "Multiple extra detected for dependency %r in version %r required " "by %r in version %r from index %r with marker %r, only the " "first extra will be used: %r", dependency["package_name"], dependency_version, package_name, package_version, index_url, dependency.get("marker"), dependency.get("extra"), ) DependsOn.get_or_create( session, version=python_package_version, entity=dependency_entity, version_range=dependency.get("required_version") or "*", marker=dependency.get("marker"), extra=dependency["extra"][0] if dependency.get("extra") else None, marker_evaluation_result=dependency.get("marker_evaluation_result", True), ) for error_info in document["result"]["errors"]: # Normalized in `_create_python_package_version'. package_name = error_info.get("package_name") or error_info["package"] package_version = error_info.get("package_version") or error_info["version"] index_url = error_info.get("index_url") or error_info["index"] _LOGGER.info( "Syncing solver errors for package %r in version %r from %r found by solver %r", package_name, package_version, index_url, solver_info, ) # Sync to PPV table only packages that are provided, regardless solving errors. The default # value of True is due to legacy thoth-solver output. python_package_version_id = None if error_info.get("is_provided_package_version", True): python_package_version_id = self._create_python_package_version( session, package_name, package_version, os_name=ecosystem_solver.os_name, os_version=ecosystem_solver.os_version, python_version=ecosystem_solver.python_version, index_url=index_url, ).id solved, _ = Solved.get_or_create( session, datetime=solver_datetime, document_id=solver_document_id, version_id=python_package_version_id, ecosystem_solver=ecosystem_solver, duration=solver_duration, error=True, error_unparseable=False, error_unsolvable=False, is_provided=python_package_version_id is not None, ) for unsolvable in document["result"]["unresolved"]: if not unsolvable["version_spec"].startswith("==="): # No resolution can be performed so no identifier is captured, report warning and continue. # We would like to capture this especially when there are # packages in ecosystem that we cannot find (e.g. not configured private index # or removed package). _LOGGER.warning( "Cannot sync unsolvable package %r as package is not locked to as specific version", unsolvable ) continue package_name = self.normalize_python_package_name(unsolvable["package_name"]) index_url = unsolvable.get("index_url") or unsolvable["index"] package_version = self.normalize_python_package_version(unsolvable["version_spec"][len("===") :]) _LOGGER.info( "Syncing unsolvable package %r in version %r from %r found by solver %r", package_name, package_version, index_url, solver_info, ) python_package_version = self._create_python_package_version( session, package_name, package_version, os_name=ecosystem_solver.os_name, os_version=ecosystem_solver.os_version, python_version=ecosystem_solver.python_version, index_url=index_url, ) solved, _ = Solved.get_or_create( session, datetime=solver_datetime, document_id=solver_document_id, version_id=python_package_version.id, ecosystem_solver=ecosystem_solver, duration=solver_duration, error=True, error_unparseable=False, error_unsolvable=True, ) for unparsed in document["result"]["unparsed"]: parts = unparsed["requirement"].rsplit("===", maxsplit=1) if len(parts) != 2: # This request did not come from graph-refresh job as there is not pinned version. _LOGGER.warning( "Cannot sync unparsed package %r as package is not locked to as specific version", unparsed ) continue package_name, package_version = parts _LOGGER.info( "Syncing unparsed package %r in version %r from %r", package_name, package_version, solver_info ) python_package_version = self._create_python_package_version( session, package_name, package_version, os_name=ecosystem_solver.os_name, os_version=ecosystem_solver.os_version, python_version=ecosystem_solver.python_version, index_url=None, ) solved, _ = Solved.get_or_create( session, datetime=solver_datetime, document_id=solver_document_id, version=python_package_version, ecosystem_solver=ecosystem_solver, duration=solver_duration, error=True, error_unparseable=True, error_unsolvable=False, )
[docs] def sync_adviser_result(self, document: dict) -> None: """Sync adviser result into graph database.""" adviser_document_id = AdvisersResultsStore.get_document_id(document) parameters = document["result"]["parameters"] cli_arguments = document["metadata"]["arguments"]["thoth-adviser"] origin = (cli_arguments.get("metadata") or {}).get("origin") re_run_adviser_id = (cli_arguments.get("metadata") or {}).get("re_run_adviser_id") is_s2i = (cli_arguments.get("metadata") or {}).get("is_s2i") runtime_environment = parameters["project"].get("runtime_environment") source_type = (cli_arguments.get("metadata") or {}).get("source_type") source_type = source_type.upper() if source_type else None os = runtime_environment.get("operating_system", {}) if os: os_name = runtime_environment["operating_system"].get("name") if os_name: runtime_environment["operating_system"]["name"] = map_os_name( os_name=runtime_environment["operating_system"]["name"] ) need_re_run = False if not origin: _LOGGER.warning("No origin stated in the adviser result %r", adviser_document_id) if is_s2i is None: _LOGGER.warning("No s2i flag stated in the adviser result %r", adviser_document_id) with self._session_scope() as session, session.begin(subtransactions=True): external_hardware_info, external_run_software_environment = self._runtime_environment_conf2models( session, runtime_environment=runtime_environment, environment_type=EnvironmentTypeEnum.RUNTIME.value, is_external=True, ) # Input stack. external_software_stack = self._create_python_software_stack( session, requirements=parameters["project"].get("requirements"), requirements_lock=parameters["project"].get("requirements_locked"), software_environment=external_run_software_environment, is_external=True, ) attributes = { "additional_stack_info": bool(document["result"].get("stack_info")), "advised_configuration_changes": bool(document["result"].get("advised_configuration")), "adviser_document_id": adviser_document_id, "adviser_error": document["result"]["error"], "adviser_name": document["metadata"]["analyzer"], "adviser_version": document["metadata"]["analyzer_version"], "count": parameters["count"], "datetime": document["metadata"]["datetime"], "debug": cli_arguments.get("verbose", False), "duration": document["metadata"].get("duration"), "limit": parameters["limit"], "limit_latest_versions": parameters.get("limit_latest_versions"), "origin": origin, "source_type": source_type, "is_s2i": is_s2i, "recommendation_type": parameters["recommendation_type"].upper(), "requirements_format": parameters["requirements_format"].upper(), "external_hardware_information_id": external_hardware_info.id, "external_build_software_environment_id": None, "external_run_software_environment_id": external_run_software_environment.id, "user_software_stack_id": external_software_stack.id, } # Output stacks - advised stacks if not document["result"].get("report", {}): _LOGGER.warning("No report found in %r", adviser_document_id) adviser_run, _ = AdviserRun.get_or_create(session, **attributes, need_re_run=need_re_run) return unresolved_packages = document["result"].get("report", {}).get("_ERROR_DETAILS", {}).get("unresolved", []) if unresolved_packages: need_re_run = True if re_run_adviser_id and unresolved_packages: # If adviser was re run and there are still unsolved packages. adviser_run, _ = AdviserRun.get_or_create( session, **attributes, need_re_run=need_re_run, re_run_adviser_id=re_run_adviser_id ) elif re_run_adviser_id and not unresolved_packages: # If adviser was re run and there are no more unsolved packages. # Modify initial adviser flag in order to avoid re run. first_adviser_run = ( session.query(AdviserRun).filter(AdviserRun.adviser_document_id == re_run_adviser_id).first() ) # INSERT…ON CONFLICT (Upsert) # https://docs.sqlalchemy.org/en/13/dialects/postgresql.html?highlight=conflict#insert-on-conflict-upsert # https://docs.sqlalchemy.org/en/13/errors.html#sql-expression-language compile required if first_adviser_run and first_adviser_run.need_re_run: insert_stmt = insert(AdviserRun).values(**first_adviser_run.to_dict(without_id=False)) do_update_stmt = insert_stmt.on_conflict_do_update( index_elements=["id"], set_=dict(need_re_run=False) ) session.execute(do_update_stmt) # Store current adviser run. adviser_run, _ = AdviserRun.get_or_create( session, **attributes, need_re_run=need_re_run, re_run_adviser_id=re_run_adviser_id ) else: # Any other case of adviser run. adviser_run, _ = AdviserRun.get_or_create(session, **attributes, need_re_run=need_re_run) advised_stacks = [] for idx, product in enumerate(document["result"].get("report", {}).get("products", [])): performance_score = None overall_score = product["score"] for entry in product.get("justification", []): if "performance_score" in entry: if performance_score is not None: _LOGGER.error( "Multiple performance score entries found in %r (index: %d)", adviser_document_id, idx ) performance_score = entry["performance_score"] if product.get("project", {}).get("requirements_locked"): advised_software_stack = self._create_python_software_stack( session, software_stack_type=SoftwareStackTypeEnum.ADVISED.value, requirements=product["project"]["requirements"], requirements_lock=product["project"]["requirements_locked"], software_environment=external_run_software_environment, performance_score=performance_score, overall_score=overall_score, ) Advised.get_or_create( session, adviser_run_id=adviser_run.id, python_software_stack_id=advised_software_stack.id, ) advised_stacks.append(advised_software_stack) if source_type == "KEBECHET" and advised_stacks: slug = "/".join( origin.split( "/", )[-2:] ) _LOGGER.info("Kebechet reference slug is %r", slug) kebechet_installed = ( session.query(KebechetGithubAppInstallations) .filter(KebechetGithubAppInstallations.slug == slug) .first() ) if kebechet_installed: insert_stmt = insert(KebechetGithubAppInstallations).values( **kebechet_installed.to_dict(without_id=False) ) do_update_stmt = insert_stmt.on_conflict_do_update( index_elements=["id"], set_=dict( last_run=document["metadata"]["datetime"], thoth_advise_manager=True, advised_python_software_stack_id=advised_stacks[0].id, ), ) session.execute(do_update_stmt) else: _LOGGER.warning("No Kebechet installation found for %r", origin) # Mark down packages that were not solved if adviser run failed. for unresolved in unresolved_packages: python_package_version_entity = self._create_python_package_version( session, package_name=unresolved, package_version=None, index_url=None, os_name=None, os_version=None, python_version=None, sync_only_entity=True, ) HasUnresolved.get_or_create( session, adviser_run_id=adviser_run.id, python_package_version_entity_id=python_package_version_entity.id, )
[docs] def sync_provenance_checker_result(self, document: dict) -> None: """Sync provenance checker results into graph database.""" provenance_checker_document_id = ProvenanceResultsStore.get_document_id(document) origin = (document["metadata"]["arguments"]["thoth-adviser"].get("metadata") or {}).get("origin") if not origin: _LOGGER.warning("No origin stated in the provenance-checker result %r", provenance_checker_document_id) with self._session_scope() as session, session.begin(subtransactions=True): parameters = document["result"]["parameters"] software_stack = self._create_python_software_stack( session, requirements=parameters["project"].get("requirements"), requirements_lock=parameters["project"].get("requirements_locked"), software_environment=None, is_external=True, ) provenance_checker_run, _ = ProvenanceCheckerRun.get_or_create( session, provenance_checker_document_id=provenance_checker_document_id, datetime=document["metadata"]["datetime"], provenance_checker_version=document["metadata"]["analyzer_version"], provenance_checker_name=document["metadata"]["analyzer"], origin=origin, debug=document["metadata"]["arguments"]["thoth-adviser"]["verbose"], provenance_checker_error=document["result"]["error"], duration=document["metadata"].get("duration"), user_software_stack_id=software_stack.id, ) # Mark down packages that were not solved and missed in provenance checker. report = document["result"]["report"] for package in report: # Discover unresolved package matching the message ID if package["id"] == "MISSING-PACKAGE": python_package_version_entity = self._create_python_package_version( session, package_name=package["package_name"], package_version=package["package_version"].lstrip("=="), index_url=package["source"]["url"], os_name=None, os_version=None, python_version=None, sync_only_entity=True, )
[docs] def sync_dependency_monkey_result(self, document: dict) -> None: """Sync reports of dependency monkey runs.""" if "ERROR" in document["result"]["report"]: _LOGGER.warning( "No entries to be synced for Dependency Monkey %r as Dependency Monkey failed", DependencyMonkeyReportsStore.get_document_id(document), ) return with self._session_scope() as session, session.begin(subtransactions=True): parameters = document["result"]["parameters"] run_hardware_information, run_software_environment = self._runtime_environment_conf2models( session, parameters["project"].get("runtime_environment", {}), environment_type=EnvironmentTypeEnum.RUNTIME.value, is_external=False, ) build_hardware_information, build_software_environment = self._runtime_environment_conf2models( session, parameters["project"].get("runtime_environment", {}), environment_type=EnvironmentTypeEnum.BUILDTIME.value, is_external=False, ) dependency_monkey_run, _ = DependencyMonkeyRun.get_or_create( session, dependency_monkey_document_id=DependencyMonkeyReportsStore.get_document_id(document), datetime=document["metadata"]["datetime"], dependency_monkey_name=document["metadata"]["analyzer"], dependency_monkey_version=document["metadata"]["analyzer_version"], seed=parameters.get("seed"), decision=parameters.get("decision_type"), count=parameters.get("count"), limit_latest_versions=parameters.get("limit_latest_versions"), debug=document["metadata"]["arguments"]["thoth-adviser"]["verbose"], dependency_monkey_error=document["result"]["error"], duration=document["metadata"].get("duration"), build_software_environment_id=build_software_environment.id, build_hardware_information_id=build_hardware_information.id, run_software_environment_id=run_software_environment.id, run_hardware_information_id=run_hardware_information.id, ) python_package_requirements = self._create_python_package_requirement( session, parameters["project"].get("requirements") ) for python_package_requirement in python_package_requirements: PythonDependencyMonkeyRequirements.get_or_create( session, python_package_requirement_id=python_package_requirement.id, dependency_monkey_run_id=dependency_monkey_run.id, ) # Number of times each inspection run will be run count = document["result"]["parameters"]["count"] for entry in document["result"]["report"]["responses"]: inspection_document_id = entry["response"] for inspection_result_number in range(count): inspection_run = ( session.query(InspectionRun) .filter(InspectionRun.inspection_document_id == inspection_document_id) .filter(InspectionRun.inspection_result_number == inspection_result_number) .filter(InspectionRun.dependency_monkey_run_id == dependency_monkey_run.id) .first() ) if inspection_run is None: inspection_run = InspectionRun( inspection_document_id=inspection_document_id, inspection_sync_state=InspectionSyncStateEnum.PENDING.value, inspection_result_number=inspection_result_number, dependency_monkey_run_id=dependency_monkey_run.id, ) session.add(inspection_run)
[docs] @lru_cache(maxsize=_GET_PYTHON_PACKAGE_REQUIRED_SYMBOLS_CACHE_SIZE) def get_python_package_required_symbols(self, package_name: str, package_version: str, index_url: str) -> List[str]: """Get required symbols for a Python package in a specified version.""" package_name = self.normalize_python_package_name(package_name) package_version = self.normalize_python_package_version(package_version) index_url = self.normalize_python_index_url(index_url) with self._session_scope() as session: query = ( session.query(PythonPackageVersionEntity) .filter(PythonPackageVersionEntity.package_name == self.normalize_python_package_name(package_name)) .filter( PythonPackageVersionEntity.package_version == self.normalize_python_package_version(package_version) ) .join(PythonPackageIndex) .filter(PythonPackageIndex.url == index_url) .join(HasArtifact) .join(RequiresSymbol, HasArtifact.python_artifact_id == RequiresSymbol.python_artifact_id) .join(VersionedSymbol) .with_entities(VersionedSymbol.symbol) .distinct(VersionedSymbol.symbol) ) # Query returns list of single tuples # NOTE: can be empty even if request is valid return [i[0] for i in query.all()]
[docs] def get_analyzed_image_symbols_all( self, os_name: str, os_version: str, *, python_version: Optional[str] = None, cuda_version: Optional[str] = None ) -> List[str]: """Get symbols associated with a given image.""" os_name = map_os_name(os_name) with self._session_scope() as session: query = ( session.query(SoftwareEnvironment) .filter(SoftwareEnvironment.os_name == os_name) .filter(SoftwareEnvironment.os_version == normalize_os_version(os_name, os_version)) .filter(SoftwareEnvironment.cuda_version == cuda_version) .filter(SoftwareEnvironment.python_version == python_version) .join(HasSymbol) .join(VersionedSymbol) .with_entities(VersionedSymbol.symbol) .distinct(VersionedSymbol.symbol) ) # Query returns list of single tuples (empty if bad request) return [i[0] for i in query.all()]
[docs] @lru_cache(maxsize=_GET_S2I_ANALYZED_IMAGE_SYMBOLS) def get_thoth_s2i_analyzed_image_symbols_all( self, thoth_s2i_image_name: str, thoth_s2i_image_version: str, is_external: bool = False ) -> List[str]: """Get symbols associated with a given Thoth s2i container image.""" model = ExternalSoftwareEnvironment if is_external else SoftwareEnvironment with self._session_scope() as session: query = ( session.query(model) .filter(model.thoth_s2i_image_name == thoth_s2i_image_name) .filter(model.thoth_s2i_image_version == thoth_s2i_image_version) .join(HasSymbol) .join(VersionedSymbol) .with_entities(VersionedSymbol.symbol) .distinct(VersionedSymbol.symbol) ) # Query returns list of single tuples (empty if bad request) return [i[0] for i in query.all()]
[docs] def get_thoth_s2i_all(self, is_external: bool = False) -> List[Tuple[str, str]]: """Get all the Thoth s2i container images available.""" model = ExternalSoftwareEnvironment if is_external else SoftwareEnvironment with self._session_scope() as session: query = ( session.query(model) .with_entities(model.thoth_s2i_image_name, model.thoth_s2i_image_version) .distinct(model.thoth_s2i_image_name, model.thoth_s2i_image_version) ) # Query returns list of single tuples (empty if bad request) return [tuple(i) for i in query.all()]
[docs] def get_thoth_s2i_package_extract_analysis_document_id_all( self, thoth_s2i_image_name: str, thoth_s2i_image_version: str, is_external: bool = False ) -> List[str]: """Get package-extract analysis ids for the given Thoth s2i.""" model = ExternalSoftwareEnvironment if is_external else SoftwareEnvironment with self._session_scope() as session: query = ( session.query(PackageExtractRun) .join(model) .filter(model.thoth_s2i_image_name == thoth_s2i_image_name) .filter(model.thoth_s2i_image_version == thoth_s2i_image_version) .with_entities(PackageExtractRun.analysis_document_id) ) return [i[0] for i in query.all()]
[docs] def get_pi_count(self, component: str) -> Dict[str, int]: """Get dictionary with number of Performance Indicators per type for the PI component selected.""" result = {} with self._session_scope() as session: for pi_model in PERFORMANCE_MODELS_ML_FRAMEWORKS: result[pi_model.__tablename__] = session.query(pi_model).filter_by(component=component).count() return result
[docs] def get_entity_count(self, entity: Union[Base, BaseExtension]) -> int: """Get count of a specific entity in the database.""" with self._session_scope() as session: result = session.query(func.count(entity.id)).scalar() return result
[docs] def get_performance_table_count(self) -> Dict[str, int]: """Get dictionary mapping performance tables to records count.""" result = {} with self._session_scope() as session: for performance_model in ALL_PERFORMANCE_MODELS: result[performance_model.__tablename__] = session.query(func.count(performance_model.id)).scalar() return result
[docs] def get_main_table_count(self) -> Dict[str, int]: """Retrieve dictionary mapping main tables to records count.""" result = {} with self._session_scope() as session: for main_model in ALL_MAIN_MODELS: result[main_model.__tablename__] = session.query(func.count(main_model.id)).scalar() return result
[docs] def get_relation_table_count(self) -> Dict[str, int]: """Retrieve dictionary mapping relation tables to records count.""" result = {} with self._session_scope() as session: for relation_model in ALL_RELATION_MODELS: result[relation_model.__tablename__] = session.query(relation_model).count() return result
[docs] def get_pi_component_all(self) -> List[str]: """Retrieve pi components in Thoth database.""" result = [] with self._session_scope() as session: for performance_model in PERFORMANCE_MODELS_ML_FRAMEWORKS: query = session.query(performance_model).with_entities(performance_model.component).distinct() result = result + query.all() return list(set([r[0] for r in result]))
[docs] def stats(self) -> dict: """Get statistics for this adapter.""" stats = {} # We need to provide name explicitly as wrappers do not handle it correctly. for method in self._CACHED_METHODS: stats[method.__name__] = dict(method.cache_info()._asdict()) return {"memory_cache_info": stats}
[docs] def cache_clear(self) -> None: """Drop cache of records.""" for method in self._CACHED_METHODS: method.cache_clear()
[docs] def get_database_size(self) -> int: """Get size of the database in bytes.""" query = ( f"SELECT pg_database_size(pg_database.datname) AS size_in_bytes FROM " f"pg_database WHERE pg_database.datname='{self._engine.url.database}'" ) with self._session_scope() as session: result = session.execute(query).fetchone() return result[0]
[docs] def is_database_corrupted(self) -> bool: """ Run the amcheck extension to check for DB corruption, false negatives are possible but false positives are not. amcheck documenation: https://www.postgresql.org/docs/10/amcheck.html Returns ------- bool False: No DB corruption detected by amcheck (not definitive) True: Database is corrupted """ check_for_ext_query = "SELECT * FROM pg_extension WHERE extname='amcheck'" run_amcheck_query = """SELECT bt_index_check(index => c.oid), c.relname, c.relpages FROM pg_index i JOIN pg_opclass op ON i.indclass[0] = op.oid JOIN pg_am am ON op.opcmethod = am.oid JOIN pg_class c ON i.indexrelid = c.oid WHERE am.amname = 'btree' -- Don't check temp tables, which may be from another session: AND c.relpersistence != 't' -- Function may throw an error when this is omitted: AND c.relkind = 'i' AND i.indisready AND i.indisvalid""" with self._session_scope() as session: if list(session.execute(check_for_ext_query)) == []: _LOGGER.error("amcheck extension not found.") return False # do not want to accidentally mistake this state with the DB being corrupted try: session.execute(run_amcheck_query) return False except Exception as e: _LOGGER.error(e) return True
[docs] def get_index_bloat_data(self) -> List[Dict[str, Any]]: """Get index bloat data. documenation: https://raw.githubusercontent.com/pgexperts/pgx_scripts/master/bloat/index_bloat_check.sql It returns data for each index/table present in the database. Examples: >>> from thoth.storages import GraphDatabase >>> graph = GraphDatabase() >>> graph.get_index_bloat_data() [ { 'database_name': 'postgres', 'schema_name': 'public', 'table_name': 'depends_on', 'index_name': 'depends_on_entity_id_idx', 'bloat_pct': 11.0, 'bloat_mb': 623.0, 'index_mb': 5821.516, 'table_mb': 14053.625, 'index_scans': 2 }, { 'database_name': 'postgres', 'schema_name': 'public', 'table_name': 'python_package_version', 'index_name': 'python_package_version_package_name_package_version_python__key', 'bloat_pct': 43.0, 'bloat_mb': 35.0, 'index_mb': 35.0, 'table_mb': 111.344, 'index_scans': 0 }, ... ] """ # btree index stats query estimates bloat for btree indexes btree_index_atts = """SELECT nspname, indexclass.relname as index_name, indexclass.reltuples, indexclass.relpages, indrelid, indexrelid, indexclass.relam, tableclass.relname as tablename, regexp_split_to_table(indkey::text, ' ')::smallint AS attnum, indexrelid as index_oid FROM pg_index JOIN pg_class AS indexclass ON pg_index.indexrelid = indexclass.oid JOIN pg_class AS tableclass ON pg_index.indrelid = tableclass.oid JOIN pg_namespace ON pg_namespace.oid = indexclass.relnamespace JOIN pg_am ON indexclass.relam = pg_am.oid WHERE pg_am.amname = 'btree' and indexclass.relpages > 0 AND nspname NOT IN ('pg_catalog','information_schema')""" index_item_sizes = """SELECT ind_atts.nspname, ind_atts.index_name, ind_atts.reltuples, ind_atts.relpages, ind_atts.relam, indrelid AS table_oid, index_oid, current_setting('block_size')::numeric AS bs, 8 AS maxalign, 24 AS pagehdr, CASE WHEN max(coalesce(pg_stats.null_frac,0)) = 0 THEN 2 ELSE 6 END AS index_tuple_hdr, sum( (1-coalesce(pg_stats.null_frac, 0)) * coalesce(pg_stats.avg_width, 1024) ) AS nulldatawidth FROM pg_attribute JOIN btree_index_atts AS ind_atts ON pg_attribute.attrelid = ind_atts.indexrelid AND pg_attribute.attnum = ind_atts.attnum JOIN pg_stats ON pg_stats.schemaname = ind_atts.nspname -- stats for regular index columns AND ( (pg_stats.tablename = ind_atts.tablename AND pg_stats.attname = pg_catalog.pg_get_indexdef(pg_attribute.attrelid, pg_attribute.attnum, TRUE)) -- stats for functional indexes OR (pg_stats.tablename = ind_atts.index_name AND pg_stats.attname = pg_attribute.attname)) WHERE pg_attribute.attnum > 0 GROUP BY 1, 2, 3, 4, 5, 6, 7, 8, 9""" index_aligned_est = """SELECT maxalign, bs, nspname, index_name, reltuples, relpages, relam, table_oid, index_oid, coalesce ( ceil ( reltuples * ( 6 + maxalign - CASE WHEN index_tuple_hdr%maxalign = 0 THEN maxalign ELSE index_tuple_hdr%maxalign END + nulldatawidth + maxalign - CASE /* Add padding to the data to align on MAXALIGN */ WHEN nulldatawidth::integer%maxalign = 0 THEN maxalign ELSE nulldatawidth::integer%maxalign END )::numeric / ( bs - pagehdr::NUMERIC ) +1 ) , 0 ) as expected FROM index_item_sizes""" raw_bloat = """SELECT curren