Fixes #96, #101, #99 and belbio/bel_sources#96

Fixed issue with equivalencing - both the issue of slow equivalencing due to using up to 10 steps for equivalences and the issue that alt_ids were not included in equivalencing.

Also fixed the issue with dashes and underscores being used to tokenize text for term completion - now we only use colons and spaces for tokenization.

Also shifted api routes into a separate file.

CHANGELOG.md

@@ -1,61 +1,28 @@
-# Change Log
+# Changelog
+All notable changes to the BELbio API will be documented in this file.
 
-## [Unreleased](https://github.com/belbio/bel_api/tree/HEAD)
+The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
+and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
-[Full Changelog](https://github.com/belbio/bel_api/compare/v0.2.0...HEAD)
 
-**Closed issues:**
+## [Unreleased]
+[Full Commit Log](https://github.com/belbio/bel_api/compare/v0.4.3...HEAD)
 
-- Refactor term completion [\#50](https://github.com/belbio/bel_api/issues/50)
-- Medline processing [\#46](https://github.com/belbio/bel_api/issues/46)
+### Added
+-
 
-## [v0.2.0](https://github.com/belbio/bel_api/tree/v0.2.0) (2018-01-21)
-[Full Changelog](https://github.com/belbio/bel_api/compare/v0.1.2...v0.2.0)
+### Changed
+-
 
-## [v0.1.2](https://github.com/belbio/bel_api/tree/v0.1.2) (2018-01-08)
-[Full Changelog](https://github.com/belbio/bel_api/compare/v0.1.1...v0.1.2)
+### Fixed
+- BEL terms - whitespace tokenization in ES for terms like IL-6
 
-## [v0.1.1](https://github.com/belbio/bel_api/tree/v0.1.1) (2018-01-08)
-**Fixed bugs:**
+## [0.4.3]  Aug 16, 2018
+[Full Commit Log](https://github.com/belbio/bel_api/compare/v0.3.1...v0.4.3)
 
-- nested statements [\#35](https://github.com/belbio/bel_api/issues/35)
-- Ortholog bug - bad species\_id results in 500 error [\#25](https://github.com/belbio/bel_api/issues/25)
+### Changed
+- Serving Swagger from BEL API codebase instead of separate documentation location
 
-**Closed issues:**
-
-- Allow setting custom canonical/decanonical targets [\#32](https://github.com/belbio/bel_api/issues/32)
-- Evaluate 204 instead of 404 [\#29](https://github.com/belbio/bel_api/issues/29)
-- Pluralize all routes [\#28](https://github.com/belbio/bel_api/issues/28)
-- Re-work Config.py [\#27](https://github.com/belbio/bel_api/issues/27)
-- Ortholog response [\#26](https://github.com/belbio/bel_api/issues/26)
-- Evaluate adding Swagger UI to Falcon [\#24](https://github.com/belbio/bel_api/issues/24)
-- Generate semantic classes using the YAML file [\#14](https://github.com/belbio/bel_api/issues/14)
-- Swap name/abbrev in yaml file [\#13](https://github.com/belbio/bel_api/issues/13)
-- BEL-LANG pop\(\) [\#12](https://github.com/belbio/bel_api/issues/12)
-- BEL-LANG Add label to subject/object [\#11](https://github.com/belbio/bel_api/issues/11)
-- BEL-LANG Add gene mod\_func [\#10](https://github.com/belbio/bel_api/issues/10)
-- Create namespace/annotation terminology files [\#9](https://github.com/belbio/bel_api/issues/9)
-- Create gene scaffold BEL statements [\#8](https://github.com/belbio/bel_api/issues/8)
-- Create orthology BEL statements [\#7](https://github.com/belbio/bel_api/issues/7)
-- Add LIC file to project root [\#5](https://github.com/belbio/bel_api/issues/5)
-- Add py.test skeleton [\#4](https://github.com/belbio/bel_api/issues/4)
-- Create Terminology JSON Schema [\#3](https://github.com/belbio/bel_api/issues/3)
-- Create API specification [\#1](https://github.com/belbio/bel_api/issues/1)
-
-**Merged pull requests:**
-
-- Bump elasticsearch from 5.4.0 to 6.0.0 [\#34](https://github.com/belbio/bel_api/pull/34) ([dependabot[bot]](https://github.com/apps/dependabot))
-- Bump python-arango from 3.11.0 to 3.12.1 [\#30](https://github.com/belbio/bel_api/pull/30) ([dependabot[bot]](https://github.com/apps/dependabot))
-- updated schemas [\#22](https://github.com/belbio/bel_api/pull/22) ([wshayes](https://github.com/wshayes))
-- Updated nanopub jsonschema [\#21](https://github.com/belbio/bel_api/pull/21) ([wshayes](https://github.com/wshayes))
-- Bump PyJWT from 1.5.2 to 1.5.3 [\#20](https://github.com/belbio/bel_api/pull/20) ([dependabot[bot]](https://github.com/apps/dependabot))
-- Bump falcon from 1.1.0 to 1.3.0rc2 [\#19](https://github.com/belbio/bel_api/pull/19) ([dependabot[bot]](https://github.com/apps/dependabot))
-- Bump elasticsearch from 5.1.0 to 5.4.0 [\#18](https://github.com/belbio/bel_api/pull/18) ([dependabot[bot]](https://github.com/apps/dependabot))
-- Bump gunicorn from 19.6.0 to 19.7.1 [\#16](https://github.com/belbio/bel_api/pull/16) ([dependabot[bot]](https://github.com/apps/dependabot))
-- Bump PyJWT from 1.4.2 to 1.5.2 [\#15](https://github.com/belbio/bel_api/pull/15) ([dependabot[bot]](https://github.com/apps/dependabot))
-- Added py.test skeleton/instructions [\#6](https://github.com/belbio/bel_api/pull/6) ([wshayes](https://github.com/wshayes))
-- Contribution guidelines [\#2](https://github.com/belbio/bel_api/pull/2) ([wshayes](https://github.com/wshayes))
-
-
-
-\* *This Change Log was automatically generated by [github_changelog_generator](https://github.com/skywinder/Github-Changelog-Generator)*
+### Fixed
+- Fixed term completion species_id bug
+- Added missing parameters to Swagger docs