dccvalidator is intended to be customizable for different settings. The Shiny application uses a configuration file to set details such as where to store uploaded files, which metadata templates to validate against, whom to contact with questions, etc.
To create a custom version of the app, you’ll need to follow these steps:
config.ymlfile. Note that any values you do not customize will be inherited from the default configuration. The configuration file must have a
app.R, replace the
"default"configuration with the name of your new configuration.
To install the dccvalidator instead of forking the repository:
app.Rfile containing the following:
config.ymlfile using the configuration options specified below and name the parameters “default”.
default: parent: "syn20400157"
parent: The Synapse project or folder where files will be stored
path_to_markdown: Location of an R Markdown document with app instructions. If you wish to omit instructions, insert
study_table: Synapse ID of a table that lists all of the existing studies in the consortium. It should have a column called
annotations_table: Synapse ID of a table that lists allowable annotation keys and values for the consortium. This should follow the same basic format as our Synapse Annotations table, e.g. there must be the following columns:
annotations_link: URL to a list or description of allowable annotation values (so users can read more)
templates_link: URL to the location of metadata templates
study_link_animal: URL to an example study description for an animal model study
study_link_human: URL to an example study description for a human study
teams: The team(s) a user must be a member of in order to use the app. If the user is not in any of the teams, they will see a message telling them they must be added to one of the teams.
assay_templates): Synapse IDs of templates to use for validation. These should be either .xlsx or .csv files, where the column names reflect the required columns in the template. If the template is an excel file with multiple sheets, the first sheet will be used.
species_list: List of possible species in the consortium. These are shown as options in the validation UI and control which individual template and biospecimen template the app validates against.
complete_columns: For each metadata file and the manifest, a list of the columns that must be complete (i.e. not contain any missing values or empty strings)
contact_email: Email address linked in footer for users to contact if they have questions