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
• 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    • has been replaced by info service in ott plugin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    • I'm pretty sure this is obsolete, need to verify with stephen.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    • Has this also been superseded by getMRCA?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
  • getSynthesisSourceList -> (remove)
    • add this functionality to draft_tree_info
    • *** WARNING: this is used by Jim ***
  • 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
  • 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