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DSI

The DataSHIELD Interface. Virtual classes to be implemented for accessing data repositories and base functions to be used by DS clients.

https://github.com/datashield/dsi

Science Score: 13.0%

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    Low similarity (11.3%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

The DataSHIELD Interface. Virtual classes to be implemented for accessing data repositories and base functions to be used by DS clients.

Basic Info
Statistics
  • Stars: 2
  • Watchers: 9
  • Forks: 6
  • Open Issues: 5
  • Releases: 12
Created over 7 years ago · Last pushed over 1 year ago
Metadata Files
Readme License

README.md

DataSHIELD Interface

CRAN_Status_Badge

The DataSHIELD Interface (DSI) defines a set of S4 classes and generic methods that can be implemented for accessing a data repository supporting the DataSHIELD infrastructure: controlled R commands to be executed on the server side are garanteeing that non disclosive information is returned to client side.

Learn more about DataSHIELD.

Class Structure

The DSI classes are:

  • DSObject a common base class for all DSI,
  • DSDriver drives the creation of a connection object,
  • DSConnection allows the interaction with the remote server; DataSHIELD operations such as aggregation and assignment return a result object; DataSHIELD setup status check can be performed (dataset access, configuration comparision),
  • DSResult wraps access to the result, which can be fetched either synchronously or asynchronously depending on the capabilities of the data repository server.

All classes are virtual: they cannot be instantiated directly and instead must be subclassed. See DSOpal for a reference implementation of DSI based on the Opal data warehouse. See also DSLite for a server-less implementation of DSI for local datasets.

These S4 classes and generic methods are meant to be used for implementing connection to a DataSHIELD-aware data repository.

Higher Level Functions

In addition to these S4 classes, DSI provides functions to handle a list of remote data repository servers:

  • datashield.login and datashield.logout will make use of the DSDriver paradigm to create DSConnections to the data repositories,
  • datashield.aggregate and datashield.assign will perform typical DataSHIELD operations on DSConnections, which result will be fetched through DSResult objects,
  • datashield.connections, datashield.connections_default and datashield.connections_find are functions for managing the list of DSConnection objects that will be discovered and used by the client-side analytic functions.
  • datashield.errors will report the last R errors that may have occurred after a datashield.assign or datashield.aggregate call.
  • Other data management functions are provided by the DSConnection objects:
    • datashield.workspaces, datashield.workspace_save, datashield.workspace_restore and datashield.workspace_rm allow to manage R images of the remote DataSHIELD sessions (to speed up data analysis sessions),
    • datashield.symbols and datashield.symbol_rm offer a minimalistic management of the R symbols living in the remote DataSHIELD sessions,
    • datashield.tables, datashield.table_status list the tables and their accessibility across a set of data repositories,
    • datashield.resources, datashield.resource_status list the resources and their accessibility across a set of data repositories,
    • datashield.pkg_status, datashield.method_status and datashield.methods are utility functions to explore the DataSHIELD setup across a set of data repositories.
    • datashield.profiles lists the DataSHIELD profiles that can be selected at login time.

These datashield.* functions are meant to be used by DataSHIELD packages developers and users.

Options

Some options can be set to modify the behavior of the DSI:

  • datashield.env is the R environment in which the DSConnection object list is to be looking for. Default value is the Global Environment: globalenv().
  • datashield.progress is a logical to enable the visibility of the progress bars. Default value is TRUE.
  • datashield.progress.clear is a logical to make the progress bar disappear after it has been completed. Default value is FALSE.
  • datashield.errors.stop is a logical to alter error handling behavior: if TRUE an error is raised when at least one server has failed, otherwise a warning message is issued. Default value is TRUE.
  • datashield.errors.print is a logical for controlling the error print in the console: if TRUE the errors are automatically printed in rich text, otherwise subsequent call to datashield.errors() is required to get the details of the errors. Default value is FALSE.
  • datashield.polling.sleep.0 time in seconds to wait before checking async calls completion, before ~1 second. Default value 50 milliseconds.
  • datashield.polling.sleep.1 base time in seconds to wait before checking async calls completion, after ~1 second. Default value is 1 second.
  • datashield.polling.sleep.10 time in seconds to wait before checking async calls completion, after ~10 seconds. Default value is x2 the base time (2 seconds).
  • datashield.polling.sleep.60 time in seconds to wait before checking async calls completion, after ~1 minute. Default value is x10 the base time (10 seconds).
  • datashield.polling.sleep.600 time in seconds to wait before checking async calls completion, after ~10 minutes. Default value is x60 the base time (1 minute).
  • datashield.polling.sleep.3600 time in seconds to wait before checking async calls completion, after ~1 hour. Default value is x600 the base time (10 minutes).

Owner

  • Name: DataSHIELD
  • Login: datashield
  • Kind: organization
  • Email: datashield@liverpool.ac.uk

DataSHIELD is a series of R libraries that enables the non-disclosive co-analysis of distributed sensitive research data.

GitHub Events

Total
  • Issue comment event: 3
  • Push event: 2
  • Pull request event: 1
  • Pull request review event: 2
  • Create event: 1
Last Year
  • Issue comment event: 3
  • Push event: 2
  • Pull request event: 1
  • Pull request review event: 2
  • Create event: 1

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 108
  • Total Committers: 2
  • Avg Commits per committer: 54.0
  • Development Distribution Score (DDS): 0.019
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Yannick Marcon y****n@o****g 106
sidohaakma s****o@h****g 2
Committer Domains (Top 20 + Academic)
haakma.org: 1 obiba.org: 1

Issues and Pull Requests

Last synced: 12 months ago

All Time
  • Total issues: 15
  • Total pull requests: 5
  • Average time to close issues: about 1 month
  • Average time to close pull requests: about 1 month
  • Total issue authors: 7
  • Total pull request authors: 3
  • Average comments per issue: 2.07
  • Average comments per pull request: 1.4
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: 18 days
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 5.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • ymarcon (8)
  • davraam (2)
  • fdlk (1)
  • StuartWheater (1)
  • timcadman (1)
  • IulianD (1)
  • ESCRI11 (1)
Pull Request Authors
  • timcadman (3)
  • ymarcon (2)
  • sidohaakma (1)
Top Labels
Issue Labels
enhancement (9) bug (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 1,032 last-month
  • Total docker downloads: 22,070
  • Total dependent packages: 3
  • Total dependent repositories: 29
  • Total versions: 10
  • Total maintainers: 1
cran.r-project.org: DSI

'DataSHIELD' Interface

  • Versions: 10
  • Dependent Packages: 3
  • Dependent Repositories: 29
  • Downloads: 1,032 Last month
  • Docker Downloads: 22,070
Rankings
Dependent repos count: 5.0%
Forks count: 10.8%
Dependent packages count: 10.9%
Downloads: 15.5%
Average: 16.2%
Docker downloads count: 27.4%
Stargazers count: 27.8%
Maintainers (1)
yannick.marcon@obiba.org
Last synced: 12 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.1 depends
  • R6 * depends
  • methods * depends
  • progress * depends
  • testthat >= 2.1.0 suggests