Merge pull request #240 from ga4gh-beacon/develop

Release 1.0.1
ga4gh-beacon · Nov 21, 2018 · 46f5693 · 46f5693
2 parents 7dc0284 + dbea5dd
commit 46f5693
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Showing 2 changed files with 25 additions and 14 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -16,14 +16,14 @@ before_install:
   - cd ..
 
   # build swagger-parser
-  - git clone --branch=2.0 https://github.com/swagger-api/swagger-parser.git
+  - git clone --branch=v2.0.0 https://github.com/swagger-api/swagger-parser.git
   - cd swagger-parser
   - git reset --hard 7ce0f756364acee3262444ab998e9fe0963382b3
   - mvn install -DskipTests=true -Dmaven.javadoc.skip=true -B -V
   - cd ..
 
   # build swagger-inflector
-  - git clone --branch=2.0 https://github.com/swagger-api/swagger-inflector.git
+  - git clone --branch=v1.0.16 https://github.com/swagger-api/swagger-inflector.git
   - cd swagger-inflector
   - git reset --hard 421fedb162b9e9b781671bc7757ee78eb6d1f793
   - mvn install -DskipTests=true -Dmaven.javadoc.skip=true -B -V

diff --git a/beacon.yaml b/beacon.yaml
@@ -31,7 +31,7 @@ paths:
       operationId: getBeaconAlleleResponse
       parameters:
         - name: referenceName
-          description: 'Reference name (chromosome). Accepting values 1-22, X, Y.'
+          description: 'Reference name (chromosome). Accepting values 1-22, X, Y, MT.'
           in: query
           required: true
           schema:
@@ -55,35 +55,45 @@ paths:
           description: |
             Minimum start coordinate
             * startMin + startMax + endMin + endMax
-              - for querying imprecise positions (e.g. identifying all structural variants starting anywhere between startMin <-> startMax, and ending anywhere between endMin <-> endMax
-              - single or douple sided precise matches can be achieved by setting startMin = startMax XOR endMin = endMax
+              - for querying imprecise positions (e.g. identifying all structural variants starting anywhere between startMin <-> startMax, and ending anywhere between endMin <-> endMax)
+              - single or double sided precise matches can be achieved by setting startMin = startMax XOR endMin = endMax
           in: query
           schema:
-            type: string
+            type: integer
+            format: int64
+            minimum: 0
         - name: startMax
           description: |
             Maximum start coordinate. See startMin.
           in: query
           schema:
-            type: string
+            type: integer
+            format: int64
+            minimum: 0
         - name: end
           description: |
             Precise end coordinate (0-based, exclusive). See start.
           in: query
           schema:
-            type: string
+            type: integer
+            format: int64
+            minimum: 0
         - name: endMin
           description: |
             Minimum end coordinate. See startMin.
           in: query
           schema:
-            type: string
+            type: integer
+            format: int64
+            minimum: 0
         - name: endMax
           description: |
             Maximum end coordinate. See startMin.
           in: query
           schema:
-            type: string
+            type: integer
+            format: int64
+            minimum: 0
         - name: referenceBases
           description: >
             Reference bases for this variant (starting from `start`). Accepted
@@ -265,6 +275,7 @@ components:
         - '22'
         - 'X'
         - 'Y'
+        - 'MT'
     Beacon:
       type: object
       required:
@@ -343,7 +354,7 @@ components:
           $ref: '#/components/schemas/Chromosome'
         start:
           description: |
-            Precise start coordinate position, allele locus (0-based).
+            Precise start coordinate position, allele locus (0-based, inclusive).
             * start only:
               - for single positions, e.g. the start of a specified sequence alteration where the size is given through the specified alternateBases
               - typical use are queries for SNV and small InDels
@@ -354,14 +365,14 @@ components:
           format: int64
           minimum: 0
         end:
-          description: Precise end coordinate. See start.
+          description: Precise end coordinate (0-based, exclusive). See start.
           type: integer
         startMin:
           description: |
             Minimum start coordinate
             * startMin + startMax + endMin + endMax
-              - for querying imprecise positions (e.g. identifying all structural variants starting anywhere between startMin <-> startMax, and ending anywhere between endMin <-> endMax
-              - single or douple sided precise matches can be achieved by setting startMin = startMax XOR endMin = endMax
+              - for querying imprecise positions (e.g. identifying all structural variants starting anywhere between startMin <-> startMax, and ending anywhere between endMin <-> endMax)
+              - single or double sided precise matches can be achieved by setting startMin = startMax XOR endMin = endMax
           type: integer
         startMax:
           description: Maximum start coordinate. See startMin.