From 539816f9057436bac4840e63dc36f2d2fab861ab Mon Sep 17 00:00:00 2001 From: Sabela Date: Fri, 28 Sep 2018 12:34:33 +0200 Subject: [PATCH 1/9] Add support for mitochondrial DNA (#155). --- beacon.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/beacon.yaml b/beacon.yaml index 383e0e86..5881ebf3 100644 --- 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: @@ -265,6 +265,7 @@ components: - '22' - 'X' - 'Y' + - 'MT' Beacon: type: object required: From 6168ac0be1859caed8958a99abb18990305072c5 Mon Sep 17 00:00:00 2001 From: Sabela Date: Wed, 3 Oct 2018 16:38:14 +0200 Subject: [PATCH 2/9] Add missing clarification (issue #213). --- beacon.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/beacon.yaml b/beacon.yaml index 383e0e86..70957280 100644 --- a/beacon.yaml +++ b/beacon.yaml @@ -343,7 +343,7 @@ 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 @@ -354,7 +354,7 @@ 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: | From a564d8183a00333a196501fb1632ea1a5fa2d9a0 Mon Sep 17 00:00:00 2001 From: Sabela Date: Wed, 3 Oct 2018 17:01:13 +0200 Subject: [PATCH 3/9] Fix typo (issue #215) --- beacon.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/beacon.yaml b/beacon.yaml index 383e0e86..275da8ed 100644 --- a/beacon.yaml +++ b/beacon.yaml @@ -56,7 +56,7 @@ paths: 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 + - single or double sided precise matches can be achieved by setting startMin = startMax XOR endMin = endMax in: query schema: type: string @@ -361,7 +361,7 @@ components: 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 + - 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. From 843aa7f205fa9d2509b925bc5002cc80c85582e8 Mon Sep 17 00:00:00 2001 From: Sabela Date: Thu, 4 Oct 2018 14:29:03 +0200 Subject: [PATCH 4/9] Add missing parenthesis (issue #218) --- beacon.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/beacon.yaml b/beacon.yaml index 383e0e86..199fc8c1 100644 --- a/beacon.yaml +++ b/beacon.yaml @@ -55,7 +55,7 @@ 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 + - 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 in: query schema: @@ -360,7 +360,7 @@ components: 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 + - 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 type: integer startMax: From 9be8c2e3396c50e2a248098cdc02cd039f8ce0b9 Mon Sep 17 00:00:00 2001 From: teemukataja Date: Thu, 1 Nov 2018 14:10:05 +0200 Subject: [PATCH 5/9] fix deprecated swagger-parser version which makes travis builds fail --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 74f55f9b..66dfa6a0 100644 --- a/.travis.yml +++ b/.travis.yml @@ -16,7 +16,7 @@ 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 From 0a830e4f6bae4ea3e0b495d2c94bf57fcb2b3fbe Mon Sep 17 00:00:00 2001 From: Michael Baudis Date: Mon, 12 Nov 2018 16:16:33 +0100 Subject: [PATCH 6/9] type fixes for StartMin etc. The coordinates for all but the `start` parameter (`end`, `start_min`, `start_max`, `end_min`, `end_max`) were __string__ in `query`. They have be set to the values below. ``` type: integer format: int64 minimum: 0 ``` --- beacon.yaml | 20 +++++++++++++++----- 1 file changed, 15 insertions(+), 5 deletions(-) diff --git a/beacon.yaml b/beacon.yaml index 199fc8c1..1314fd5b 100644 --- a/beacon.yaml +++ b/beacon.yaml @@ -59,31 +59,41 @@ paths: - single or douple 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 From 4672d02d06ea45204e9b2571ccb3ac66aa07f07b Mon Sep 17 00:00:00 2001 From: Sabela Date: Tue, 13 Nov 2018 12:27:11 +0100 Subject: [PATCH 7/9] Point to tags instead of branches (issue #232) --- .travis.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index 66dfa6a0..d8385e27 100644 --- a/.travis.yml +++ b/.travis.yml @@ -23,14 +23,14 @@ before_install: - 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 - cd .. # build and start validator-badge - - git clone --branch=2.0 https://github.com/swagger-api/validator-badge.git + - git clone --branch=v1.0.3 https://github.com/swagger-api/validator-badge.git - cd validator-badge - mvn package -DskipTests=true -Dmaven.javadoc.skip=true -B -V jetty:run & - cd .. From cb732ea7f46514cce4479fecf6df5f93c435a025 Mon Sep 17 00:00:00 2001 From: Sabela Date: Tue, 13 Nov 2018 12:48:41 +0100 Subject: [PATCH 8/9] There is no tag which allows to validate against the OpenAPI v3. Restoring to branch 2.0 of this repo. --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index d8385e27..f6acda0f 100644 --- a/.travis.yml +++ b/.travis.yml @@ -30,7 +30,7 @@ before_install: - cd .. # build and start validator-badge - - git clone --branch=v1.0.3 https://github.com/swagger-api/validator-badge.git + - git clone --branch=2.0 https://github.com/swagger-api/validator-badge.git - cd validator-badge - mvn package -DskipTests=true -Dmaven.javadoc.skip=true -B -V jetty:run & - cd .. From 91a306b8b1b4bbc399ff095c35cde04fec06fc6a Mon Sep 17 00:00:00 2001 From: Sabela Date: Tue, 20 Nov 2018 09:07:17 +0100 Subject: [PATCH 9/9] Fix typo reintroduced by mistake when solving the conflict (#215) --- beacon.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/beacon.yaml b/beacon.yaml index 4bbf8017..d2fcebe5 100644 --- a/beacon.yaml +++ b/beacon.yaml @@ -56,7 +56,7 @@ paths: 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 + - single or double sided precise matches can be achieved by setting startMin = startMax XOR endMin = endMax in: query schema: type: string @@ -362,7 +362,7 @@ components: 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 + - 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.