Changelog

Source: NEWS.md

MsBackendMetaboLights 1.7

MsBackendMetaboLights 1.7.10

• Fix syncing data files replacing the metadata of all previously cached files, which could then no longer be found offline (with mtbls_cached_data_files() or offline = TRUE). The metadata is now merged with the existing content (issue #29).
• Data files cached with previous versions that are no longer found offline need to be synced once online again (e.g. with mtbls_sync_data_files() using the same fileName) to become available offline. Files are not downloaded again.

MsBackendMetaboLights 1.7.9

• Fix assay IDs being computed from the selected assays only (assayName), causing files with the same name in different assays to overwrite each other when assays were synced individually (issue #27).

MsBackendMetaboLights 1.7.8

• Add sleep/delay calls to vignette to reduce failures on Bioconductor build systems.

MsBackendMetaboLights 1.7.7

• Internal refactoring to reduce need to load BiocFileCache repeatedly.

MsBackendMetaboLights 1.7.6

• Add 5 second pause to examples.

MsBackendMetaboLights 1.7.5

• Fix installation instructions.
• Add 4 second pause to several unit tests trying to avoid MetaboLights connection errors.

MsBackendMetaboLights 1.7.4

• Support/handle duplicated file names across multiple assays.

MsBackendMetaboLights 1.7.3

• Support parameter fileName in backendInitialize() to load only selected file(s).

MsBackendMetaboLights 1.7.2

• Append the MetaboLights data set ID to locally stored/cached file names to avoid overwriting files with same names in different data sets.
• Enforce ordering of returned file names in alphabetic order.

MsBackendMetaboLights 1.7.1

• Fix issue white spaces in ftp link (issue [#16]).

MsBackendMetaboLights 1.5

MsBackendMetaboLights 1.5.3

• Use MsCoreUtils::retry() instead of the internal implementation.
• Improve fail-safe mechanism when caching MS data from MetaboLights.

MsBackendMetaboLights 1.5.2

• Add helper functions mtbls_assay_data(), mtbls_sample_data() and mtbls_metadata().

MsBackendMetaboLights 1.5.1

• Increase number of download retries and increase waiting time in between.
• Export the retry() function.

MsBackendMetaboLights 1.3

Changes in 1.3.2

• Support backendMerge() (issue #10).

Changes in 1.3.1

• Fix download/sync of files with BiocFileCache.

MsBackendMetaboLights 1.1

Changes in 1.1.4

• Remove debug message.

Changes in 1.1.3

• Add mtbls_delete_cache() to delete locally cached files for a specified MetaboLights ID.
• Change unit tests to only remove selected content instead of wiping the full cache.

Changes in 1.1.2

• Fetch and cache each data file individually.
• Retry retrieval of data from MetaboLights up to 3 times before throwing an error message, with an increasing time period between attempts.

MsBackendMetaboLights 1.0

Changes in 1.0.1

• Complete unit test coverage.

MsBackendMetaboLights 0.99

Changes in 0.99.1

• Add mtbls_sync() to synchronize a MsBackendMetaboLights object.
• Add mtbls_sync_data_files() function to cache selected files and mtbls_cached_data_files() to list all locally cached data files.

Changes in 0.99.0

• Prepare package for submission to Bioconductor.

MsBackendMetabolights 0.0

Changes in 0.0.3

• Add vignette and backendMerge,MsBackendMetaboLights function.

Changes in 0.0.2

• Add MsBackendMetaboLights class, constructor and backendInitalize() method.

Changes in 0.0.1

• Add utility functions to retrieve information from MetaboLights.