Update to work with latest zenodo API #81
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Tests will likely fail because of other issues being worked on |
This was referenced Oct 16, 2023
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Closed
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Couple of things...
Shall I update |
OK I just updated |
dfalster
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Oct 16, 2023
- As documented in #79 , the Zenodo API has changed, breaking our download feature. - This commit updates the internals to work with the latest changes. Specifically: - the way to access json for all versions has changed (changed url structure, and for id we now use one of the record ids, rather than the conceptid) - the call to download file has changed - format of the API json has changed Also - added record id to the table of versions - put a check in to remove "v" from any version entered by user
fontikar
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Nov 21, 2023
* changes required for v5 austraits.build * Removed original_name for trait_pivot_wider3 for v5.0.0 * Added trait_pivot_wider for v4.x.x and code for what_version * Making new switches for join and as_wide_table based on new versioning * Sub switch for extract_ and recreated internal data * Sub switches for trait_pivot_longer * Minor fix in join_methods * Added vars a global vars * Removed .data calls when not needed * Update to work with latest zenodo API (#81) - As documented in #79 , the Zenodo API has changed, breaking our download feature. - This commit updates the internals to work with the latest changes. Specifically: - the way to access json for all versions has changed (changed url structure, and for id we now use one of the record ids, rather than the conceptid) - the call to download file has changed - format of the API json has changed Also - added record id to the table of versions - put a check in to remove "v" from any version entered by user * Recreated data so extract is passing * Update `treatment_id` with `treatment_context_id` * Revert "Update `treatment_id` with `treatment_context_id`" This reverts commit 3fc6717. * minor column name changes Changes column names, reflecting recent changes to traits.build output. * Update as_wide_table.R add `any_of` to column selection within `as_wide_table` to accommodate other traits.build databases that don't have the same columns in taxon_list.csv * Fixed getting versions and load austraits with zenodo updates and minor update with as_wide_table with removal of variable * Fixed minor bug in get_version_latest --------- Co-authored-by: Elizabeth Wenk <ehwenk@gmail.com> Co-authored-by: Daniel Falster <daniel.falster@unsw.edu.au> Co-authored-by: yangsophieee <sophie.yang917@gmail.com>
fontikar
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Nov 22, 2023
* #60 fixed imports for pivot_wider, organised tests, currently not working for new version, waiting for austraits.build update * Minor naming adjustments in test * Change some dependencies to imports Some packages needed to make plots are included in suggests. This means that core functions of package may not work. * Remove helper functions to vignettes * Update deprecated functions * Restructure tests to run faster - reuse outputs from previous function calls to reduce runtime - reduce dataset sizes for slow functions (summarise_trait_means, trait_pivot_wider, plot_locations) - silence some outputs closes #62 * Change GH actions triggers * ensure consistent ordering of rows * bumped version number * Update to work with latest zenodo API (#81) - As documented in #79 , the Zenodo API has changed, breaking our download feature. - This commit updates the internals to work with the latest changes. Specifically: - the way to access json for all versions has changed (changed url structure, and for id we now use one of the record ids, rather than the conceptid) - the call to download file has changed - format of the API json has changed Also - added record id to the table of versions - put a check in to remove "v" from any version entered by user * Pulled files we want to develop from change-v5 * Changes for v5 austraits.build (#78) * changes required for v5 austraits.build * Removed original_name for trait_pivot_wider3 for v5.0.0 * Added trait_pivot_wider for v4.x.x and code for what_version * Making new switches for join and as_wide_table based on new versioning * Sub switch for extract_ and recreated internal data * Sub switches for trait_pivot_longer * Minor fix in join_methods * Added vars a global vars * Removed .data calls when not needed * Update to work with latest zenodo API (#81) - As documented in #79 , the Zenodo API has changed, breaking our download feature. - This commit updates the internals to work with the latest changes. Specifically: - the way to access json for all versions has changed (changed url structure, and for id we now use one of the record ids, rather than the conceptid) - the call to download file has changed - format of the API json has changed Also - added record id to the table of versions - put a check in to remove "v" from any version entered by user * Recreated data so extract is passing * Update `treatment_id` with `treatment_context_id` * Revert "Update `treatment_id` with `treatment_context_id`" This reverts commit 3fc6717. * minor column name changes Changes column names, reflecting recent changes to traits.build output. * Update as_wide_table.R add `any_of` to column selection within `as_wide_table` to accommodate other traits.build databases that don't have the same columns in taxon_list.csv * Fixed getting versions and load austraits with zenodo updates and minor update with as_wide_table with removal of variable * Fixed minor bug in get_version_latest --------- Co-authored-by: Elizabeth Wenk <ehwenk@gmail.com> Co-authored-by: Daniel Falster <daniel.falster@unsw.edu.au> Co-authored-by: yangsophieee <sophie.yang917@gmail.com> * Bumped version number and updated news * Added references to packages * Updated version for GH steps * Updated v number for GHA * Expanding testing suite to all 3 major versions of AusTraits (#86) * Created lites for all main versions of AusTraits * Passing for as_wide_table * Passing for as_wide_table and for extract_ * expanding test suite to all 3 majors, switches for method id adjusted * expanding test suite to all 3 majors for summarise_D * Expanding these for all 3 versions * Added PR trigger for dev branch * Added codecov yml * Setting limit for patch cov --------- Co-authored-by: Daniel Falster <daniel.falster@unsw.edu.au> Co-authored-by: Elizabeth Wenk <ehwenk@gmail.com> Co-authored-by: yangsophieee <sophie.yang917@gmail.com>
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As documented in #79 , the Zenodo API seems to have changed, breaking our download feature.
This commit updates the internals to work with the latest changes.
Specifically:
Also