Function reference • dccvalidator

Data validation functions Functions to perform data validation and QA/QC checks, and report results as successes, warnings, or failures.
`check_all()`	Run all validation checks
`check_annotation_keys()`	Check annotation keys
`check_annotation_values()`	Check annotation values
`valid_annotation_keys()`	Valid annotation keys
`valid_annotation_values()`	Valid annotation values
`check_keys()`	Check that a given set of keys are all present in an annotations dictionary
`check_values()`	Check a set of keys and their values
`can_coerce()`	Check coercibility
`check_col_names()` `check_cols_manifest()` `check_cols_individual()` `check_cols_assay()` `check_cols_biospecimen()`	Check column names against their corresponding template
`check_cols_complete()`	Check for complete columns
`check_cols_empty()`	Check for empty columns
`check_files_manifest()`	Check that files are present in manifest
`check_ids_match()` `check_indiv_ids_match()` `check_specimen_ids_match()`	Check ids
`check_indiv_ids_dup()` `check_specimen_ids_dup()`	Check uniqueness of individual and specimen IDs
`check_schema_json()`	Check data against a JSON Schema
`check_schema_df()`	Check a data frame of data against a JSON Schema
`check_parent_syn()`	Check synID of parent in manifest
`check_ages_over_90()`	Check for ages over 90
`check_duplicate_paths()`	Check for duplicated file paths
`check_complete_ids()`	Check data against existing IDs
Validation helpers Functions used by the data validation functions above.
`get_synapse_annotations()`	Get Synapse annotations
`get_synapse_table()`	Get Synapse table
`get_template()`	Get metadata template keys
`get_synapse_schema()`	Get Synapse validation schema
`get_template_keys_synID()`	Get excel or csv template
`get_template_keys_schema()`	Get JSON schema template
`df_to_json_list()`	Convert data frame to JSON
`get_metadataType_indices()`	Get metadataType indices
Shiny app functions Functions to generate and run the dccvalidator Shiny application. Also includes modules that make up the app.
`run_app()`	Run the Shiny application
`app_server()`	App server
`app_ui()`	App UI
`mod_main_ui()` `mod_main_server()`	Main dccvalidator UI
`mod_synapse_oauth_ui()` `mod_synapse_oauth_server()`	Synapse Oauth Module
`with_busy_indicator_ui()` `with_busy_indicator_server()`	Show busy indicator
`results_boxes_ui()` `results_boxes_server()`	UI function for results boxes module
`file_summary_ui()` `file_summary_server()`	UI for the file summary module
`report_unsatisfied_requirements()`	Create a modal dialog if user is not in required team(s) or certified
`gather_template_ids()`	Gather all template ids
App-supporting functions Functions that the dccvalidator app uses to ensure the user is able to use the application and to provide instructions.
`check_certified_user()`	Check if user is certified
`check_team_membership()`	Check team membership
`setup_global_oauth_vars()`	Sets up global OAuth variables
`oauth_process()`	Do the OAuth process
`has_auth_code()`	Has authorization code
`attempt_login()`	Attempt to log into Synapse
`logged_in()`	Check if logged in as user
`show_modal()`	Wrapper for modals
Constructors for validation results These functions generate custom conditions for reporting check failures, warnings, and successes.
`check_condition()`	Create a condition of the given type
`check_pass()` `check_warn()` `check_fail()`	Create custom conditions for reporting
Updating metadata template dictionaries These functions validate annotations data structure, generate new dictionary sheets from the annotations, and upload new versions of the templates.
`add_dictionary_sheets()`	Add Dictionary Sheets
`get_template_synIDs()`	Get Template synIDs
`update_template_dictionaries()`	Update Template Dictionaries
`verify_dictionary_structure()`	Verify Dictionary Structure
Internal development These functions help with development needs, such as changing which Synapse endpoints to use.
`set_staging_endpoints()`	Set Synapse Staging Endpoints

Reference

Data validation functions

Validation helpers

Shiny app functions

App-supporting functions

Constructors for validation results

Updating metadata template dictionaries

Internal development