induced subtree request by id fails for genus Id

[jhpoelen]

For some reason, induced subtree can be retrieved using ott ids c(357968, 867416, 939325) , but not c(357968, 867416, 939325, 462102) .

This succeeds:

> rotl::tol_induced_subtree(ott_ids = c(357968, 867416, 939325))

Phylogenetic tree with 3 tips and 1 internal nodes.

Tip labels:
[1] "Blastophaga_nipponica_ott939325" "Blastophaga_psenes_ott357968"   
[3] "Blastophaga_quadrupes_ott867416"
Node labels:
[1] "Blastophaga_ott462102"

Unrooted; no branch lengths.
> 

but this fails:

> rotl::tol_induced_subtree(ott_ids = c(357968, 867416, 939325, 462102))
Error: HTTP failure: 500
Index: 32, Size: 32

Is this an opentree or rotl issue?

[josephwb]

Seems like an OpenTree problem:

curl -X POST http://devapi.opentreeoflife.org/v2/tree_of_life/induced_subtree -H "Content-Type:application/json" -d '{"ott_ids":[357968,867416,939325,462102]}'

{
  "message" : "Index: 32, Size: 32",
  "exception" : "IndexOutOfBoundsException",
  "fullname" : "java.lang.IndexOutOfBoundsException",
  "stacktrace" : [ "java.util.ArrayList.rangeCheck(ArrayList.java:635)", "java.util.ArrayList.get(ArrayList.java:411)", "opentree.GraphExplorer.getDraftTreeMRCAForNodes(GraphExplorer.java:360)", "opentree.GraphExplorer.extractDraftSubtreeForTipNodes(GraphExplorer.java:468)", "opentree.plugins.tree_of_life.induced_subtree(tree_of_life.java:315)", "java.lang.reflect.Method.invoke(Method.java:606)", "org.neo4j.server.plugins.PluginMethod.invoke(PluginMethod.java:57)", "org.neo4j.server.plugins.PluginManager.invoke(PluginManager.java:168)", "org.neo4j.server.rest.web.ExtensionService.invokeGraphDatabaseExtension(ExtensionService.java:300)", "org.neo4j.server.rest.web.ExtensionService.invokeGraphDatabaseExtension(ExtensionService.java:122)", "java.lang.reflect.Method.invoke(Method.java:606)", "org.neo4j.server.rest.security.SecurityFilter.doFilter(SecurityFilter.java:112)" ]
}

I hope to get this fixed today.

[jhpoelen]

Thanks!

[jhpoelen]

I've attempted to reproduce the issue, hoping to close this issue. Here's what I got:

> rotl::tol_induced_subtree(ott_ids = c(357968, 867416, 939325))

Phylogenetic tree with 3 tips and 1 internal nodes.

Tip labels:
[1] "Blastophaga_nipponica_ott939325" "Blastophaga_psenes_ott357968"   
[3] "Blastophaga_quadrupes_ott867416"
Node labels:
[1] "Blastophaga_ott462102"

Unrooted; no branch lengths.

Similar to previous result.

However:

> rotl::tol_induced_subtree(ott_ids = c(357968, 867416, 939325, 462102))
Error: HTTP failure: 500
The node Node[1846303] does not seem to be in the draft tree.

@josephwb Is this expected behavior? I was hoping that asking for subtree /w missing ott id would create subtree and perhaps indicate that some ott id was ignored because it wasn't in the draft tree.

[josephwb]

@jhpoelen No, this is not expected behaviour. A subtree should be returned, together with warnings if ids were 1) not in the synthetic tree or 2) altogether invalid ids. e.g. [edited, as there was a paste error in the curl call]:

curl -X POST http://api.opentreeoflife.org/v2/tree_of_life/induced_subtree -H "content-type:application/json" -d '{"ott_ids":[357968, 867416, 939325, 9999999]}'

{
  "subtree" : "(Blastophaga_nipponica_ott939325,Blastophaga_psenes_ott357968,Blastophaga_quadrupes_ott867416)Blastophaga_ott462102;",
  "ott_ids_not_in_tree" : [ ],
  "ott_ids_not_in_graph" : [ 9999999 ],
  "node_ids_not_in_graph" : [ ],
  "node_ids_not_in_tree" : [ ]
}

I believe what you are getting stems from an ongoing issue where one query node is the ancestor of another (can you confirm this? I can check, of course, but you probably know).

Anyway, definitely not an rOTL issue.

[jhpoelen]

@josephwb from earlier example in this thread, the first three ott ids are tips (i.e. 357968, 867416, 939325) and the last one is a node (i.e. 462102) and wasp genus Blastophaga . Hope this helps.

[josephwb]

Ok, thanks. I have fixed this bug (not yet deployed), but am working on fixing another.

[fmichonneau]

hi @josephwb

Did your fix get deployed? This still seems to fail on the OTL side (i.e., no subtree is being returned).

curl -X POST http://devapi.opentreeoflife.org/v2/tree_of_life/induced_subtree -H "Content-Type:application/json" -d '{"ott_ids":[357968,867416,939325,462102]}'
{
  "message" : "The node Node[1992344] does not seem to be in the draft tree.",
  "exception" : "UnsupportedOperationException",
  "fullname" : "java.lang.UnsupportedOperationException",
  "stacktrace" : [ "opentree.GraphExplorer.getTreeTipRootPathMap(GraphExplorer.java:326)", "opentree.GraphExplorer.extractDraftSubtreeForTipNodes(GraphExplorer.java:530)", "opentree.plugins.tree_of_life.induced_subtree(tree_of_life.java:333)", "java.lang.reflect.Method.invoke(Method.java:497)", "org.neo4j.server.plugins.PluginMethod.invoke(PluginMethod.java:57)", "org.neo4j.server.plugins.PluginManager.invoke(PluginManager.java:168)", "org.neo4j.server.rest.web.ExtensionService.invokeGraphDatabaseExtension(ExtensionService.java:300)", "org.neo4j.server.rest.web.ExtensionService.invokeGraphDatabaseExtension(ExtensionService.java:122)", "java.lang.reflect.Method.invoke(Method.java:497)", "org.neo4j.server.rest.security.SecurityFilter.doFilter(SecurityFilter.java:112)" ]
}

[josephwb]

This works.

[jhpoelen]

Thanks for fixing this!