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ymarconymarcon
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task: added linter (#44)
* Fix E501 line length issues in console.py, data.py, dictionary.py, exports.py, and file.py * Continue fixing E501 line length issues in imports.py * Fix E501 line length issues in table.py * Fix E501 line length issues in system.py * Fix E501 line length issues * Fixed remaining lint errors * fix: file download the pythonic way * chore: code cleaning * chore: code cleanup
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‎.github/workflows/ci.yml‎

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- name: Install dependencies
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run: uv sync --all-extras
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- name: Run linting
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run: uv run ruff check .
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- name: Run tests
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run: uv run pytest

‎.gitignore‎

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__pycache__
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debug.py
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.serena/
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.serena/
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plans/

‎.ruff.toml‎

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# Ruff configuration file
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# Exclude a variety of commonly ignored directories.
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extend-exclude = [
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"__pycache__",
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".git",
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".venv",
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".eggs",
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".nox",
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".tox",
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".svn",
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".hg",
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"build",
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"dist",
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".mypy_cache",
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".pytest_cache",
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]
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# Assume Python 3.10.
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target-version = "py310"
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# Line length with preview to format
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line-length = 120
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preview = true
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[lint]
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# Enable flake8-bugbear rules
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select = [
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"E", # pycodestyle errors
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"W", # pycodestyle warnings
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"F", # pyflakes
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"B", # flake8-bugbear
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"C4", # flake8-comprehensions
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"UP", # pyupgrade
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"SIM", # flake8-simplify
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]
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# Allow autofix for all enabled rules (when `--fix`) is provided.
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fixable = ["ALL"]
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# Allow unused variables when underscore-prefixed.
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dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"

‎Makefile‎

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test:
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uv run --all-extras pytest
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lint:
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uv run ruff check .
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fix:
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uv run ruff check . --fix
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format:
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uv run ruff format .
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check: format fix
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build:
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uv build
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‎obiba_opal/__init__.py‎

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from obiba_opal.core import UriBuilder, OpalClient, OpalRequest, OpalResponse, Formatter, MagmaNameResolver, HTTPError
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from obiba_opal.project import ProjectService, BackupProjectCommand, RestoreProjectCommand
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from obiba_opal.core import (
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UriBuilder,
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OpalClient,
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OpalRequest,
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OpalResponse,
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Formatter,
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MagmaNameResolver,
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HTTPError,
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)
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from obiba_opal.project import (
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ProjectService,
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BackupProjectCommand,
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RestoreProjectCommand,
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)
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from obiba_opal.table import CopyTableCommand, BackupViewService, RestoreViewService
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from obiba_opal.dictionary import DictionaryService, ExportAnnotationsService, ImportAnnotationsService
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from obiba_opal.dictionary import (
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DictionaryService,
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ExportAnnotationsService,
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ImportAnnotationsService,
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)
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from obiba_opal.data import DataService, EntityService
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from obiba_opal.analysis import AnalysisCommand, ExportAnalysisService
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from obiba_opal.file import FileService
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from obiba_opal.exports import ExportPluginCommand, ExportCSVCommand, ExportXMLCommand, ExportRSASCommand, ExportRSPSSCommand, ExportRSTATACommand, ExportRDSCommand, ExportSQLCommand, ExportVCFCommand
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from obiba_opal.exports import (
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ExportPluginCommand,
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ExportCSVCommand,
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ExportXMLCommand,
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ExportRSASCommand,
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ExportRSPSSCommand,
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ExportRSTATACommand,
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ExportRDSCommand,
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ExportSQLCommand,
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ExportVCFCommand,
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)
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from obiba_opal.subjects import UserService, GroupService
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from obiba_opal.perm import ProjectPermService, DatasourcePermService, TablePermService, VariablePermService, ResourcePermService, ResourcesPermService, RPermService, DataSHIELDPermService, SystemPermService
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from obiba_opal.imports import ImportPluginCommand, ImportCSVCommand, ImportIDMapService, ImportIDService, ImportLimeSurveyCommand, ImportOpalCommand, ImportRDSCommand, ImportRSASCommand, ImportRSPSSCommand, ImportRSTATACommand, ImportSQLCommand, ImportVCFCommand, ImportXMLCommand
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from obiba_opal.system import PluginService, SystemService, TaxonomyService, TaskService, RESTService
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from obiba_opal.perm import (
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ProjectPermService,
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DatasourcePermService,
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TablePermService,
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VariablePermService,
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ResourcePermService,
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ResourcesPermService,
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RPermService,
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DataSHIELDPermService,
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SystemPermService,
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)
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from obiba_opal.imports import (
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ImportPluginCommand,
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ImportCSVCommand,
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ImportIDMapService,
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ImportIDService,
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ImportLimeSurveyCommand,
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ImportOpalCommand,
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ImportRDSCommand,
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ImportRSASCommand,
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ImportRSPSSCommand,
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ImportRSTATACommand,
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ImportSQLCommand,
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ImportVCFCommand,
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ImportXMLCommand,
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)
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from obiba_opal.system import (
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PluginService,
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SystemService,
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TaxonomyService,
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TaskService,
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RESTService,
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)
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from obiba_opal.sql import SQLService, SQLHistoryService
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from obiba_opal.security import EncryptService, DecryptService
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__all__ = [
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"UriBuilder",
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"OpalClient",
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"OpalRequest",
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"OpalResponse",
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"Formatter",
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"MagmaNameResolver",
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"HTTPError",
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"ProjectService",
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"BackupProjectCommand",
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"RestoreProjectCommand",
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"CopyTableCommand",
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"BackupViewService",
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"RestoreViewService",
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"DictionaryService",
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"ExportAnnotationsService",
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"ImportAnnotationsService",
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"DataService",
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"EntityService",
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"AnalysisCommand",
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"ExportAnalysisService",
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"FileService",
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"ExportPluginCommand",
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"ExportCSVCommand",
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"ExportXMLCommand",
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"ExportRSASCommand",
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"ExportRSPSSCommand",
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"ExportRSTATACommand",
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"ExportRDSCommand",
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"ExportSQLCommand",
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"ExportVCFCommand",
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"UserService",
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"GroupService",
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"ProjectPermService",
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"DatasourcePermService",
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"TablePermService",
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"VariablePermService",
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"ResourcePermService",
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"ResourcesPermService",
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"RPermService",
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"DataSHIELDPermService",
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"SystemPermService",
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"ImportPluginCommand",
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"ImportCSVCommand",
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"ImportIDMapService",
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"ImportIDService",
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"ImportLimeSurveyCommand",
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"ImportOpalCommand",
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"ImportRDSCommand",
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"ImportRSASCommand",
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"ImportRSPSSCommand",
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"ImportRSTATACommand",
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"ImportSQLCommand",
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"ImportVCFCommand",
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"ImportXMLCommand",
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"PluginService",
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"SystemService",
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"TaxonomyService",
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"TaskService",
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"RESTService",
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"SQLService",
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"SQLHistoryService",
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"EncryptService",
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"DecryptService",
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]

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