_pkgdown.yml

template:
  params:
    bootswatch: flatly

reference:
- title: Data validation functions
  desc: >
    Functions to perform data validation and QA/QC checks, and report results as
    successes, warnings, or failures.
  contents:
    - check_all
    - check_annotation_keys
    - check_annotation_values
    - valid_annotation_keys
    - valid_annotation_values
    - check_keys
    - check_values
    - can_coerce
    - check_col_names
    - check_cols_manifest
    - check_cols_individual
    - check_cols_assay
    - check_cols_biospecimen
    - check_cols_complete
    - check_cols_empty
    - check_files_manifest
    - check_ids_match
    - check_indiv_ids_match
    - check_specimen_ids_match
    - check_indiv_ids_dup
    - check_specimen_ids_dup
    - check_schema_json
    - check_schema_df
    - check_parent_syn
    - check_ages_over_90
    - check_duplicate_paths
    - check_complete_ids
    - check_invalid_characters

- title: Validation helpers
  desc: >
    Functions used by the data validation functions above.
  contents:
    - get_synapse_annotations
    - get_synapse_table
    - get_template
    - get_synapse_schema
    - get_template_keys_synID
    - get_template_keys_schema
    - df_to_json_list
    - get_metadataType_indices

- title: Shiny app functions
  desc: >
    Functions to generate and run the dccvalidator Shiny application. Also
    includes modules that make up the app.
  contents:
    - run_app
    - app_server
    - app_ui
    - mod_main_ui
    - mod_main_server
    - mod_synapse_oauth_ui
    - mod_synapse_oauth_server
    - with_busy_indicator_ui
    - with_busy_indicator_server
    - results_boxes_ui
    - results_boxes_server
    - file_summary_ui
    - file_summary_server
    - report_unsatisfied_requirements
    - gather_template_ids

- title: App-supporting functions
  desc: >
    Functions that the dccvalidator app uses to ensure the user is able to use
    the application and to provide instructions.
  contents:
    - check_certified_user
    - check_team_membership
    - setup_global_oauth_vars
    - oauth_process
    - has_auth_code
    - attempt_login
    - logged_in
    - show_modal

- title: Constructors for validation results
  desc: >
    These functions generate custom conditions for reporting check failures,
    warnings, and successes.
  contents:
    - check_condition
    - check_pass
    - check_warn
    - check_fail

- title: Updating metadata template dictionaries
  desc: >
    These functions validate annotations data structure, generate new dictionary
    sheets from the annotations, and upload new versions of the templates.
  contents:
    - add_dictionary_sheets
    - get_template_synIDs
    - get_file_schema
    - update_template_dictionaries
    - verify_dictionary_structure

- title: Internal development
  desc: >
    These functions help with development needs, such as changing which Synapse
    endpoints to use.
  contents:
    - set_staging_endpoints