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Proposed API changes 2014 08
Joseph W. Brown edited this page Aug 28, 2014
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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
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- has been replaced by info service in ott plugin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
- subtree -> subtree
- 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- I'm pretty sure this is obsolete, need to verify with stephen.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
- updateGraphFromPhylografter -> (remove?)
- 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- Has this also been superseded by getMRCA?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, while the other method specify the internal node where the tree should be subsetted.
- 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