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_pkgdown.yml
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_pkgdown.yml
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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