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Kohulansriramkanakam87
Kohulan
and
sriramkanakam87
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v3.7.0
* feat: added token-based limiter. * feat: applied limiter to the needed routes. * feat: tests in place for the token based limiter. * feat: env token is added to the yml files. * feat: enhanced CDK depictions * fix: main cleanup * fix: detailed linting * fix: abbreviations usage * fix: docstrings for abbreviations * feat: detailed tests for 2D depictions enhanced * fix: tests and radical perception along with title * fix: test coverage * fix: extended tests better coverage * fix: abbreviation tests * fix: abbreviation tests * feat: enhanced 2D depictions based on CDK * feat: fix radicals CDK * fix: templates * fix: rendering of radical images * fix: rendering of radical images debug * fix: mounted the env instead of fetching a single value. (#686) * fix: mounted the env instead of fetching a single value. * fix: mounted env in the rest of the yml files. * feat: added env example. --------- Co-authored-by: Sagar <sriramkanakam87@gmail.com> Co-authored-by: Sri Ram Sagar Kanakam <90332705+sriramkanakam87@users.noreply.github.com>
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‎.env.example‎

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# Authentication token for rate limiting bypass
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CMS_INTERNAL_AUTH_TOKEN=

‎app/dependencies.py‎

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‎app/limiter.py‎

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import os
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from slowapi import Limiter, _rate_limit_exceeded_handler
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from slowapi.errors import RateLimitExceeded
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from slowapi.util import get_remote_address
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from starlette.requests import Request as StarletteRequest
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INTERNAL_AUTH_TOKEN = os.getenv("CMS_INTERNAL_AUTH_TOKEN")
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def custom_rate_limit_key_func(request: StarletteRequest):
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"""
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Custom key function for rate limiting.
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- Authenticated requests get unique keys to effectively bypass rate limiting
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- Other requests are rate limited by IP address
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"""
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token = request.headers.get("x-internal-auth")
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# Check for valid authentication token
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if token and INTERNAL_AUTH_TOKEN and token == INTERNAL_AUTH_TOKEN:
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# Return a unique key for each authenticated request
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# This effectively bypasses rate limiting since each request gets its own bucket
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return f"auth_bypass_{id(request)}"
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# For unauthenticated requests, use IP-based rate limiting
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return get_remote_address(request)
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limiter = Limiter(key_func=custom_rate_limit_key_func)
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rate_limit_exceeded_handler = _rate_limit_exceeded_handler
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RateLimitExceededExc = RateLimitExceeded

‎app/main.py‎

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from __future__ import annotations
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# Import limiter and related objects from the shared limiter module
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from app.limiter import limiter, rate_limit_exceeded_handler, RateLimitExceededExc
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import os
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from fastapi import FastAPI
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from fastapi import status
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from fastapi_versioning import VersionedFastAPI
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from prometheus_fastapi_instrumentator import Instrumentator
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from typing import Dict
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from slowapi.middleware import SlowAPIMiddleware
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from .routers import chem
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from .routers import converters
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version=os.getenv("RELEASE_VERSION", "1.0"),
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)
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# Add middleware AFTER VersionedFastAPI creation
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app.state.limiter = limiter
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app.add_exception_handler(RateLimitExceededExc, rate_limit_exceeded_handler)
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app.add_middleware(SlowAPIMiddleware)
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Instrumentator().instrument(app).expose(app)
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origins = ["*"]

‎app/modules/cdk_depict/__init__.py‎

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"""CDK Enhancement Modules for Chemical Depiction.
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This package provides advanced CDK-based functionality for molecular depiction:
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Core Functionality:
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- Hydrogen Display: Control hydrogen atom visibility (minimal, explicit, stereo, smart)
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- CXSMILES: Extended SMILES parsing with highlighting and coordinates
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- Abbreviations: Chemical group and reagent abbreviation system
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- Dative Bonds: Coordinate bond perception and display
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- Multicenter Bonds: η-complex and π-bonding support
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Advanced Features:
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- Annotations: Atom/bond numbering, mapping, CIP labels
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- Aromatic Display: Circle-in-ring (donut) representation
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- Style Presets: Color schemes for different backgrounds
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- Advanced Controls: Zoom, stroke ratio, SVG units, structure flipping
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- Reaction Arrows: Different arrow types for reactions
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Specialized:
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- Radical Perception: Unpaired electron detection
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- MDL HILITE: Highlighting from MDL/SDF files
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"""
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# Hydrogen Display
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from app.modules.cdk_depict.hydrogen_display import (
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set_hydrogen_display,
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setHydrogenDisplay,
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HydrogenDisplayType,
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)
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# CXSMILES Parser
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from app.modules.cdk_depict.cxsmiles_parser import (
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extract_cxsmiles_highlighting,
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)
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# Abbreviations
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from app.modules.cdk_depict.abbreviations import (
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ChemicalAbbreviations,
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AbbreviationMode,
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AbbreviationOptions,
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)
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# Dative Bonds
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from app.modules.cdk_depict.dative_bonds import (
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DativeBondPerception,
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DativeBondMode,
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)
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# Multicenter Bonds
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from app.modules.cdk_depict.multicenter_bonds import (
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MulticenterBonds,
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MulticenterStyle,
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)
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# Annotations
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from app.modules.cdk_depict.annotations import (
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AnnotationSystem,
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AnnotationMode,
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MAPPING_COLORS,
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)
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# Aromatic Display
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from app.modules.cdk_depict.aromatic_display import (
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AromaticDisplaySystem,
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)
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# Style Presets
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from app.modules.cdk_depict.style_presets import (
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StylePresetSystem,
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StylePreset,
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StyleConfiguration,
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STYLE_CONFIGURATIONS,
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)
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# Advanced Controls
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from app.modules.cdk_depict.advanced_controls import (
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AdvancedControls,
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SVGUnits,
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)
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# Reaction Depiction
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from app.modules.cdk_depict.reaction_depiction import (
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ReactionArrowSystem,
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ReactionArrowType,
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ARROW_ABBREV_MAP,
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)
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# Radical Perception
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from app.modules.cdk_depict.radical_perception import (
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RadicalPerception,
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)
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# MDL HILITE
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from app.modules.cdk_depict.mdl_hilite import (
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MDLHiliteParser,
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)
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__all__ = [
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# Hydrogen Display
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"set_hydrogen_display",
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"setHydrogenDisplay",
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"HydrogenDisplayType",
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# CXSMILES
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"CXSMILESParser",
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"CXSMILESData",
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"CXSMILESError",
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"StereoGroupType",
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"extract_cxsmiles_highlighting",
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# Abbreviations
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"ChemicalAbbreviations",
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"AbbreviationMode",
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"AbbreviationOptions",
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# Dative Bonds
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"DativeBondPerception",
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"DativeBondMode",
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# Multicenter Bonds
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"MulticenterBonds",
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"MulticenterStyle",
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# Annotations
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"AnnotationSystem",
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"AnnotationMode",
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"MAPPING_COLORS",
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# Aromatic Display
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"AromaticDisplaySystem",
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# Style Presets
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"StylePresetSystem",
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"StylePreset",
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"StyleConfiguration",
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"STYLE_CONFIGURATIONS",
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# Advanced Controls
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"AdvancedControls",
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"SVGUnits",
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# Reaction Depiction
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"ReactionArrowSystem",
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"ReactionArrowType",
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"ARROW_ABBREV_MAP",
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# Radical Perception
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"RadicalPerception",
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# MDL HILITE
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"MDLHiliteParser",
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]

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