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config_version: 1
package: ComptoxR
# CTX credential name -> environment variable read by the generated auth.
authentication:
ctx: ctx_api_key
# Every API uses the package request helper and gets roxygen documentation.
helper: .ct_request
documentation: true
formatter:
name: air
version: 0.11.0
# Endpoint adoption is opt-out: everything is generated unless it matches a rule here.
# Rules match paths; prefix a rule with a method ('POST ^/path$') to ban that method only.
selection:
methods: [GET, POST]
exclude:
# Server-side file standardization; GET /api/stdizer stays approved.
- 'POST ^/api/stdizer/?$'
# #354-#356: saved rule-group management and add/replace group mutations (stdizer, alerts).
- '^/api/stdizer/groups(/|$)'
- '/(add|replace)/?$'
# #356/#358: harvest and PubChem-list resolver routes without an established end-user purpose.
- '^/api/resolver/(casharvest|universalharvest|getpubchemlist)/?$'
# Service file upload and CAS preflight routes.
- '^/api/services/(caspreflight|files)/?$'
# #357: AMOS XLSX batch exports and write routes; JSON searches stay.
- '^/api/amos/(add_aqc_spectrum|add_new_fact_sheet|add_new_method|add_new_product_declaration|add_new_safety_data_sheet|analytical_qc_batch_search|batch_search)/?$'
# Curator-mode and protocol writes are not user-facing reads.
- 'POST ^/curators/(libraries|units)/?$'
- 'POST ^/reaction/editor/\{[^/]+\}$'
- 'POST ^/api/stdizer/protocols/?$'
# Resolver file exports; duplicated by the JSON routes.
- 'POST ^/api/resolver/export(-section)?/?$'
# Replaced by existing wrappers (chemical list download, hazard reports).
- 'POST ^/chemicals/chemical_DL/?$'
- 'POST ^/api/hazard/reports/?$'
# ChET login, admin and delete pages are not API.
- '^/(auth|admin)/'
- '^/chemicals/chemdelete/?$'
# #330: ChET legacy database-old pages, superseded by the current search routes.
- '^/(chemicals|reaction)/database[-_]old(/|$)'
# #330: assay creation is a write route.
- 'POST ^/api/toxprints/assays/?$'
# #356: alerts are limited to POST /api/alerts, GET /api/alerts/metadata and /version.
- '^/api/alerts(?!/(metadata|version)/?$|/?$)'
# One file per API schema; each file explains its names and per-operation settings.
services:
- apis/chemi_alerts.yml
- apis/chemi_amnb_nate.yml
- apis/chemi_amos.yml
- apis/chemi_arn_cats.yml
- apis/chemi_chet.yml
- apis/chemi_descriptors.yml
- apis/chemi_hazard.yml
- apis/chemi_mordred.yml
- apis/chemi_ncc_cats.yml
- apis/chemi_opera.yml
- apis/chemi_padel.yml
- apis/chemi_pfas_atlas.yml
- apis/chemi_pfas_cats.yml
- apis/chemi_predictor_models.yml
- apis/chemi_rdkit.yml
- apis/chemi_resolver.yml
- apis/chemi_safety.yml
- apis/chemi_search.yml
- apis/chemi_services.yml
- apis/chemi_stdizer.yml
- apis/chemi_toxprints.yml
- apis/chemi_webtest.yml
- apis/ctx_bioactivity.yml
- apis/ctx_chemical.yml
- apis/ctx_exposure.yml
- apis/ctx_hazard.yml
- apis/epi_suite.yml
- apis/pubchem.yml
callback_files:
- dev/specmill_callbacks.R
- dev/specmill_pubchem_callbacks.R