Added simple phyloreference state system #66
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
gaurav
force-pushed
the
phyloreference_status
branch
from
baa5a02 to
b121716
Compare
Is this still true? |
|
Yes, still true! I've tested this in the Curation Tool by itself, but I'd like to make sure that the status information can actually be used by the Clade Ontology. I've gotten it to the point where the status information is read and retained by the Clade Ontology scripts (phyloref/clade-ontology#32), but I still need to modify JPhyloref to take it into account when testing (phyloref/jphyloref#8). I'll submit all three pull requests for review once I have the Travis report to show that they all worked! |
…dea as a final draft.
…tool into phyloreference_status
…tool into phyloreference_status
hlapp
approved these changes
Jun 21, 2018
|
Nope, nothing controversial! Thanks for the review! |
gaurav
added a commit
to phyloref/clade-ontology
that referenced
this pull request
Jun 22, 2018
Added phyloreferences from [Wojciechowski, 2003](http://dx.doi.org/10.1016/j.sajb.2013.06.017), using the phyloreference state system to mark phyloreferences that cannot be tested (phyloref/klados#25, phyloref/klados#66). This PHYX file takes too long to process to be included into the test suite, so for now I'm placing it into its own directory (`testcases_too_slow`) -- we will figure out the best way to continuously test them in #36.
gaurav
added a commit
that referenced
this pull request
Jan 29, 2019
This allows each phyloreference to be in one of the states laid out in #25. Changes in state for each phyloreference are recorded along with a timestamp, allowing the previous history of the phyloreference to be documented. In the future, this could be extended to archive previous versions of the phyloreference or to identify who changed its state (#59). Since this pull request requires new prefixes in the PHYX file, I've also included a fix for #46 so that we include a copy of the context we need in this repository. I've incorporated Brochu 2003 as an example for demonstrating phyloreference statuses.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This allows each phyloreference to be in one of the states laid out in #25. Changes in state for each phyloreference are recorded along with a timestamp, allowing the previous history of the phyloreference to be documented. In the future, this could be extended to archive previous versions of the phyloreference or to identify who changed its state (#59).
Since this pull request requires new prefixes in the PHYX file, I've also included a fix for #46 so that we include a copy of the context we need in this repository. I've incorporated Brochu 2003 as an example for demonstrating phyloreference statuses.
This has been tested in phyloref/clade-ontology#29 and is ready to be merged.