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Mica R

R package for accessing Mica2 web services:

  • search any type of documents (variable, dataset, study, population, dce (datacollection event), network)
  • search taxonomy vocabularies and terms
  • get data access requests form configuration and listing for reporting

Installation

Requires R 3.x.

# Install dependencies
if (!require("httr")) {
  install.package(c("httr"), dependencies=TRUE)
}
# Install from source code repository
devtools::install_github("obiba/micar")

Usage

Steps:

  • open connection to Mica server
  • extract and process documents
  • close connection with Mica server

Examples:

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Version

Install

install.packages('micar')

Monthly Downloads

149

Version

1.1.1

License

GPL-3

Maintainer

Yannick Marcon

Last Published

April 10th, 2019

Functions in micar (1.1.1)

mica.networks

Get the networks
.as.rql

Utility method to build RQL atomic statement.
mica.studies

Get the studies
.flatten

Flatten a list hierarchy
mica.study.dces

Get the study data collection events
mica.study.populations

Get the study populations
.url

Utility method to build urls. Concatenates all arguments and adds a '/' separator between each element
.reportListMetrics

Display search result metrics
.post

Issues a POST form request to mica for the specified resource
.handleResponse

Default request response handler.
mica.dars

Get the data access requests
mica.vocabularies

Get the vocabularies
mica.datasets

Get the datasets
mica.dar.form

Get the data access request form
rqlNode

New RQL node
mica.dar.history

Get data access request history
.extractLabel

Extract label for locale. If not found, fallback to undefined language label (if any).
.darStatusDTOToDF

Make a list of StatusChange DTOs a data frame (applies to DARs and their amendments)
mica.dar.amendment.form

Get the data access request amendment form
mica.dar.amendment.history

Get amendment history
mica.login

Open connection with Mica
mica.logout

Close connection with Mica
.get

Issues a GET request to mica for the specified resource
mica.dar.actions

Get data access request actions
mica.dar.amendment

Get a amendment
mica.dar.amendments

Get amendments
mica.variables

Get the variables
mica.taxonomies

Get the taxonomies
mica.dar.amendments.history

Get amendments history
.append.rql

Insert some RQL statements to perform the query. TODO parse RQL properly!
mica.dar

Get a data access request
.verbose

Verbose flag
.extractLabel2

Extract label for locale. If not found, fallback to undefined language label (if any).
.authToken

Constructs the value for the Authorization header
.darDTOToDF

Make a list of DataAccessRequest DTOs a data frame (applies to DARs and their amendments)
.extractMicaSessionId

Extract micasid from cookie data frame.