ropensci / rotl

Interface to Open Tree of Life API
https://docs.ropensci.org/rotl
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Corrupted error message #96

Open rossmounce opened 7 years ago

rossmounce commented 7 years ago

I'm trying to get the subtree for Tracheophytes. It's too many tips to be available from this service but I note the error message has garbled the URL I can download the full tree from - I think it's added several "BadInputException"s

Also... could someone just snip me off the Tracheophyte clade? I'd be most grateful. Getting that from the WHOLE synthesis tree sounds like a bit of a large task. There must be quite some demand for this I would imagine. I can't be the only one?

mono_id <- tnrs_match_names("Tracheophyta")
mono_tree <- tol_subtree(ott_id = ott_id(mono_id))
Error: HTTP failure: 400
Requested tree (270012 tips) is larger than currently allowed by this service (100000 tips). For larger trees, please download the full tree directly from: http://files.opentreeoflife.org/trees/BadInputExceptionorg.neo4j.server.rest.repr.BadInputExceptionlist("opentree.plugins.tree_of_life_v3.doSubtree(tree_of_life_v3.java:691)", "opentree.plugins.tree_of_life_v3.subtree(tree_of_life_v3.java:563)", "java.lang.reflect.Method.invoke(Method.java:498)", "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:498)", "org.neo4j.server.rest.security.SecurityFilter.doFilter(SecurityFilter.java:112)")

Session info:

> sessionInfo()
R version 3.2.5 (2016-04-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] rotl_3.0.3

loaded via a namespace (and not attached):
 [1] rentrez_1.0.4   httr_1.2.1.9000 R6_2.2.0        assertthat_0.1 
 [5] parallel_3.2.5  tools_3.2.5     curl_2.3        Rcpp_0.12.8    
 [9] nlme_3.1-127    ape_4.0         grid_3.2.5      jsonlite_1.2   
[13] rncl_0.6.0      XML_3.98-1.3    lattice_0.20-33