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Changelog

Source: NEWS.md

extractox 1.2.1

Breaking Changes

  • extr_ctd and extr_tetramer have been removed from the package. The CTD website now requires an ALTCHA CAPTCHA challenge that prevents automated API access. All related source, documentation, and tests have been deleted.

New Features

  • Graceful exit on error: All exported HTTP-facing functions (extr_comptox, extr_ice, extr_iris, extr_pprtv, extr_casrn_from_cid, extr_chem_info, extr_pubchem_fema, extr_pubchem_ghs) now return NULL with a cli::cli_warn() message on failure instead of throwing an error. This is implemented via the new internal helper with_graceful_exit().
  • Jittered exponential backoff: All httr2 requests now use req_retry(max_tries = 5, backoff = httr2_backoff) with a jittered exponential backoff strategy (capped at 30 s, ±20% jitter). condathis/curl code paths use an equivalent condathis_run_retry() helper.

Bug Fixes

  • Fixed condathis::run() calls in extr_comptox_openssl_() and extr_iris_openssl_(): errors are now caught via tryCatch and re-thrown with a clear message rather than causing an uncontrolled crash.
  • Fixed extr_chem_info: now aborts with an informative message when PubChem returns an empty response, rather than failing silently downstream.
  • Fixed the httr2_backoff() function signature to match the single-argument backoff callback contract required by httr2::req_retry().
  • Restored the correct CompTox batch export endpoint URL in extr_comptox_out().
  • Fixed a typo (s. → .) in the DESCRIPTION field (#50).
  • Updated test expectations for extr_ice and extr_casrn_from_cid to match current upstream API response sizes.
  • Updated extr_comptox tests to reflect a CompTox API change: comptox_main_data now returns 63 columns instead of 64.
  • Updated extr_casrn_from_cid test to reflect current PubChem data (row count updated from 42 to 29).
  • Fixed extr_tox test: replaced incorrect expect_no_warning() with suppressWarnings(); the function intentionally warns via with_graceful_exit() when an individual sub-service (e.g. ICE) fails transiently. The data.frame check is now resilient to NULL elements from transiently unavailable services.
  • Fixed extr_monograph test: corrected expect() call to expect_equal() when checking the count of missing values.
  • Added missing skip_on_cran() and skip_if_offline() guards to extr_monograph tests that make live API calls.
  • Renamed test file test_monograph.R to test-monograph.R to follow the test-*.R convention required for automatic discovery by testthat.

extractox 1.2.0

CRAN release: 2025-07-15

Major Changes & Enhancements

  • Automated Server Compatibility: Functions connecting to EPA servers (e.g., extr_comptox, extr_iris, extr_pprtv) now automatically handle connection issues that can occur on systems with modern libcurl and OpenSSL. The functions detect problematic configurations and use the condathis package to perform requests with a compatible version of curl in an isolated environment. This ensures reliability without requiring manual user intervention.

Minor Enhancements

  • extr_chem_info now accepts the argument domain to specify the PubChem domain (substance or compound).
  • extr_tox now accepts a delay parameter to control the delay between requests, helping to avoid rate-limiting errors.
  • Request Throttling**: Added a delay parameter to PubChem functions to allow for a pause between requests, helping to avoid rate-limiting errors.
  • Verbose Option: A verbose option has been added to several functions for more detailed output during execution.

Bug Fixes

  • Testing: Corrected various tests, including a fix for an incorrect row count expectation in the PubChem test.

  • Fixed extr_chem_info duplicated name in outout columns (#47).

  • Function Cleanup: Refined the extr_comptox function, removing unnecessary requirements and cleaning up the code.

extractox 1.0.0

CRAN release: 2025-01-07

Bug Fixes

  • Fixed extr_iris extracting the correct number of chemicals without repetition (#15).
  • Fixed extr_comtox working when a single download_items different from DTXCID is selected (#17).
  • Fixed extr_casrn_from_cid failure when no results are found.

New Features

  • Added extr_ice_assay_names to retrieve ICE assay names (#16).
  • Added extr_monograph to check if a substance is listed in WHO IARC monograph and return its details (#19).
  • Added extr_pprtv to extract information from the EPA Provisional Peer-Reviewed Toxicity Values database (#20). Introduced save_to_cache and load_from_cache functions to avoid re-downloading the file each time. See force argument.

Other Breaking Changes

  • Removed cancer_types argument from extr_iris. Database returns a dataframe with different columns based on request arguments.
  • Removed stop_at_warning argument from extr_casrn_from_cid. Now warns and returns a dataframe with NA if no IDs are found.
  • extr_tox now returns a longer list of dataframes, including the outputs of extr_monograph and extr_pprtv.

Enhancements and Fixes

  • Added verbose argument to all extr_ functions (#18).
  • Unified behavior across all extr_ functions when chemicals are not found (#30-#35):
    • For all functions except extr_comptox, a query column reports the IDs searched. In extr_comptox, this info is in the main_sheet element. For extr_ice, query values contain all IDs found.
    • Results now contain rows with NA values for all columns (except query).
    • extr_pprtv and extr_monograph use save_and_match to output results with NA for missing IDs.
  • Improved and extended all unit tests.
  • extr_comptox now outputs a list of dataframes with clean names.
  • Fixed extr_ctd column names: pub_med_ids or pub_med_i_ds are now pubmed_ids.
  • Introduced extr_pubchem_section_ internal function to fetch FEMA and GHS info, avoiding repeated code.
  • Introduced check_na_warn internal function to generate warnings for missing IDs.
  • Created with_extr_sandbox to handle cache for CRAN examples.

extractox 0.1.0

CRAN release: 2024-12-03

  • Initial CRAN submission.