NEWS.md

In AmundsenJunior/pfsrsdk: Functions for interacting with Platform for Science APIs

This project follows semantic versioning

pfsrsdk 3.0.0

Known issues

• For some experiment-related pfsrsdk functions and entities related to PFS experiments, there is an issue with OData where modifications (create and update functions) are executed successfully when the PFS experiments are published. The following functions have been tested to show this behavior:
• createExperimentSample, in PFS 5.3.x and 6.0.x
• updateExperimentSampleRawData, in PFS 5.3.x and 6.0.x
• updateEntityAttributes, in PFS 5.3.x and 6.0.x
• updateEntityProject, in PFS 6.0.x

Breaking changes

• Refactored the return objects of the basic API functions (apiGET, apiPOST, apiPUT), as well as many of the SDK package functions. This was done to provide a standard return object across the SDK (where appropriate). The API functions were updated to provide a return object of structure list(content, response), where content had a value of httr::content(response). For many of the SDK functions, a standard structure of list(entity, response) was already in place, but the change here both expanded the use of this return object to other functions and updated the values of both entity and response. Refer to the package help for function-specific changes to the return objects.
• Moved useVerbose parameter on most functions to a pass-through ellipsis (...) parameter, as the parameter is only used by the underlying calls to the API functions (apiGET, apiPOST, apiPUT). Passing an argument for useVerbose must now be named, not ordered, in SDK function calls.

New functions and minor changes

• Added optional fullReturn parameter to API functions to provide option to not receive full HTTP response data in return object.
• Added function getEntityAttributeMetadata() to get attribute metadata for a specified entity type. Applicable for PFS v6 and greater.
• Added function getAttributesColumnHeaders() to get the attribute column headers for all or specified attributes of an entityType. Applicable for PFS v6 and greater.
• Added function getExperimentSamplesWithSampleLots() to get the sample lots and/or experiment samples for a particular experiment.
• Added function getExperimentContainersAndExperimentSamples() to get the experiment container, container type and experiment samples of an experiment.
• Added function getUserProjects() to get metadata of projects accessible to the current user.
• Added "semantic version" to warning, error and test messages to avoid confusion.
• Removed unnecessary headers from functions.
• Removed functions that were deprecated in pfsrsdk 1.0.0:
• getAttachedFile()
• getExperimentSamplesIntermediateData()
• ODATAcleanName()
• setExperimentSamplesAssayFileData()
• updateCellContents()
• Separated the set of API tests in test-httpFunctions.R to individual files.
• Separated acceptance tests from unit tests in the tests/testthat directory.
• Enhanced testing for functions with fullMetadata parameter.
• Enabled automated testing to ensure package compatibility with PFS 6.0.3.1 and PFS 5.3.11.
• Adjusted Jenkinsfile.decl to run acceptance tests in parallel, drastically reducing pipeline execution time.
• Added Gradle task to generate PDF manual of package documentation, via Rd2pdf.
• Corrected vignettes/TestResults.Rmd to produce properly-formatted table of test results when built as part of pkgdown::build_site() execution on Jenkins.

Fixes

• Corrected apiPUT() to check all classes of body for form_file type.
• Removed credentials from Gradle and automated testing process.

pfsrsdk 2.0.1

Fixes

• Corrected odataCleanName() to properly handle refTypes of value "tenant".

pfsrsdk 2.0.0

Breaking changes

• Fixed defect in coreAPI() that was overwriting coreAPI configuration values with environment variables. Renamed username and password configuration values to api_username and api_password to ensure compatibility with the prohibited environment variables of RStudio-Connect.
• Added parameter fullMetadata to getEntityLocation, getEntityProject, getExperimentSampleAssayData, getExperimentSamplesRawData. This changes the order of the useVerbose parameter.
• Changed default fullMetadata value.
• apiGET(), apiPOST(), apiPUT() and authBasic() will not stop the execution of the R code during an error. Warnings will show information about the error and the functions will return objects with the error details.

New functions and minor changes

• Updated license information.
• Changes and enhancements to automated internal testing.
• Updated publish functions and getAttachedAttributeFile() to use the odata options available in PFS v6.
• Updated createExperimentContainer() to warn the user when accessing a published experiment.
• Documentation updates.
• Updated updateEntityLocation() to use the InventoryMove action available in the PFS OData API.
• Removed # Completed regression for 5.3.8 and 6.0.1 message from tests.
• Added author and updated author e-mails.
• Replaced switch() with case().
• Updated packrat dependencies with newer minor versions.
• Enabled automated testing of pfsrsdk against PFS 5.3.10.
• General code cleanup
• Added useRaw parameter to apiGet() to allow raw data export.

pfsrsdk 1.0.1

Fixes

• Fixed issue where 401 error was thrown when using apiGET() and verbose is set to true.
• Fixed issue with checking to see if a particular PFS version has been tested with this package.
• Fixed issue where odataCleanName() added an underscore to the tenant alias name. (new parameter added for odataCleanName())
• Added sinking to setup.R to minimize test output.
• Added tests to test-httpFunctions.R (GET, POST, PUT) for more than 100 results.
• Added xml2 as an import since we use the httr::content() with an XML MIME type. httr only lists xml2 as "Suggest" in its DESCRIPTION.

pfsrsdk 1.0.0

PFSRSDK 1.0.0 is a major release that completely refactors the CoreAPIV2 project into the new naming convention, pfsrsdk, while updating the SDK functions for compatibility with Platform for Science (PFS) versions 5.3.8, 5.3.9, 6.0.1, and 6.0.2. Unit tests have been added to cover nearly all SDK functions and executed successfully against the listed PFS versions.

Breaking changes

• Package name coreapiv2 changed to pfsrsdk.
• Package functions called via CoreAPIV2::functionName() are now called by pfsrsdk::functionName().
• Updated coreAPI.R function, where the authentication parameters present in a user's Auth.json configuration file need to be updated:
• alias (previously TenantShortName)
• tenant (previously account)
• host (previously coreUrl)
• username (previously user)
• password (previously pwd)
• semver, a new parameter for PFS semantic version that throws a warning if not configured
• Deprecated getAttachedFile for getAttachedAttributeFile.
• Deprecated getExperimentSamplesIntermediateData for getExperimentSampleIntermediateData.
• Deprecated ODATAcleanName for odataCleanName.
• Deprecated setExperimentSamplesAssayFileData for setExperimentSampleAssayFileData.
• Deprecated updateCellContents for existing setCellContents function, as the latter provides the same functionality via PFS OData that the former executes in the PFS JSON API.

New functions and minor changes

• Added getSemVer function to test the PFS semantic version being used and adapt commands when necessary.
• Created getExperimentContainerContents to get any container contents of EXPERIMENT_CONTAINER base type.
• Created getExperimentContainerCellIds to get cell Ids of experiment containers.
• Created getExperimentWellContents to retrieve contents of a specific well in any experiment container.
• Added case utility function to provide vectorized IF operations.

Fixes

• Added packrat to package structure for dependency management.
• Added Gradle to execute package build, test, documentation process.
• Used styler to enforce clean code syntax.
• Used lintr as a tool for static code analysis.
• Added serviceRoot to coreAPI to enable SDK use against Platform Admin.
• Enabled automated testing via Jenkins against multiple versions of PFS for compatibility validation.
• Updated getContainerContents to handle generic CONTAINER contents requests.
• Created loadXmlConfigFile utility function to help prepare PFS test environments by loading application configuration files (internal calls only).
• Updated setup.r and teardown.r for tests. setup will now load the CoreApp.SDK XML in a test environement, and teardown hides information that is not needed during log out.
• Updated getWellContents to handle generic CONTAINER well content requests.
• Updated helper.r to execute against specific-version test environments without interactive prompting.

AmundsenJunior/pfsrsdk documentation built on July 18, 2019, 8:10 p.m.