Proposed API changes 2014 08

New API URLs (complete list)

taxomachine:

• tnrs/contexts
• tnrs/infer_context
• tnrs/autocomplete_query
• tnrs/context_query
• ott/subtree
• ott/info
• ott/deprecated_taxa
• ott/taxon_info
• ott/flags

treemachine:

• custom/synth_json_sas
• custom/tax_json_sas
• graph_of_life/mrca
• graph_of_life/subtree
• graph_of_life/draft_tree_info
• graph_of_life/ott_version <- should this be taxonomy_version to be more agnostic?
• graph_of_life/source_tree
• graph_of_life/draft_tree
• graph_of_life/taxon_info
• graph_of_life/draft_tree_children
• graph_of_life/node_status <- new plugin. is node 1) in graph?, 2) in synth tree?, 3) num children, 4) support trees, 5) trees that do not support node (new to formalize this), 6) other stuff?
• import/test_nexson (maybe)

oti:

• indexing/add_nexsons
• indexing/remove_nexsons
• queries/all_studies
• queries/studies
• queries/trees
• queries/nodes
• queries/properties

Proposed changes

taxomachine:

• TNRS -> tnrs
  • taxomachine/vN/tnrs/contexts
  • getContextForNames -> infer_context
  • autocompleteQuery -> autocomplete_query
  • contextQuery -> context_query
  • getTaxonomyVersion -> (remove)
    • has been replaced by info service in ott plugin
• OTTServices -> ott
  • subtree -> subtree
    • moved from getJSONs
    • may be useful, change input format to accept a list of ott ids for a pruned subtree or a single ott id for a clade subtree
  • getTaxonomyInfo -> info
  • getDeprecatedTaxa -> deprecated_taxa
  • getTaxonInfo -> taxon_info
  • getFlaggedTaxonCount -> flags
• getJSONs -> (remove)
  • getNodeIdJSONFromName -> (remove)
  • getConflictTaxJsonAltRel -> (remove)
  • subtree -> (move to ott plugin)

treemachine:

• getSASJsons -> custom
  • getSynthJson -> synth_json_sas
  • getTaxonJson -> tax_json_sas
• PhylografterUpdater -> (remove?)
  • updateGraphFromPhylografter -> (remove?)
    • I'm pretty sure this is obsolete, need to verify with stephen. if not, move to import plugin
• GoLS -> graph_of_life
  • getSourceTreeIds -> (remove)
  • getDraftTreeMRCAForNodes -> (remove?)
    • I think Joseph has replaced this with getMRCA
  • getTaxonomyMRCAForNodes -> (remove?)
    • Has this also been superseded by getMRCA? (JWB: yes. But there was a question of whether this should be 1 service or 2)
  • getMRCA -> mrca
  • getDraftSubtreeForNodes -> subtree
  • getStudyIngestMessagesForNexSON -> (either remove or move to import plugin)
  • getDraftTreeID -> draft_tree_info
    • add the info from getSynthesisSources
  • getTaxonomyVersion -> ott_version <- or 'taxonomy_version'
  • getSynthesisSourceList -> (remove)
    • add this functionality to draft_tree_info
    • *** WARNING: this is used by Jim ***
    • maybe rename to 'source_list'?
  • synthesizeSubtree -> (remove)
    • this initiates a synthesis procedure. not something we want exposed right now
  • getSourceTree -> source_tree
  • getSyntheticTree -> draft_tree
    • we may want to combine this with the getsubtree method...
  • getDraftTreeForottId -> (remove?)
    • combine this with the subtree method
  • getDraftTreeForNodeIdD -> (remove)
    • combine this with the subtree method
    • *** I may be missing something here. subtree seems to specify the set of tip taxa requested (e.g. duck, human, turtle, sunflower), while the other methods specify the internal node where the tree should be subsetted (e.g. Aves).
  • getNodeIdForottId -> taxon_info
  • getDraftTreeChildNodesForNodeID -> draft_children
• (new, maybe) -> import
  • getStudyIngestMessagesForNexSON -> test_nexson (potentially moved from GoLS)

oti:

• ConfigurationServices -> (remove - these are unused and not for public use anyway)
  • install OTT -> (remove)
  • connectAllTreesToOTT -> (remove)
• IndexServices -> indexing (NOTE: these should not be part of the public api...)
  • indexNexsons -> add_nexsons
  • unindexNexsons -> remove_nexsons
• NexsonServices -> (remove; empty)
• QueryServices -> queries
  • findAllStudies -> all_studies
  • singlePropertySearchForStudies -> studies
  • singlePropertySearchForTrees -> trees
  • singlePropertySearcgForTreeNodes -> nodes
  • getSearchablePropertiesStudies -> properties
  • getSearchablePropertiesForTrees -> (remove)
    • add info to properties
  • getSearchablePropertiesForTreeNodes -> (remove)
    • add info to properties