From 0d8486acd7556737f3b0ff4babb8e3dfc2211ec9 Mon Sep 17 00:00:00 2001
From: Andrew Olson <olson@cshl.edu>
Date: Fri, 18 Mar 2016 17:56:27 -0400
Subject: [PATCH] speciestree

---
 api/swagger/swagger.yaml | 92 +++++++++++++++++++++++++++++++++++++++-
 npm-shrinkwrap.json      | 12 +++---
 package.json             |  2 +-
 3 files changed, 98 insertions(+), 8 deletions(-)

diff --git a/api/swagger/swagger.yaml b/api/swagger/swagger.yaml
index 5ce3938..4d948e0 100644
--- a/api/swagger/swagger.yaml
+++ b/api/swagger/swagger.yaml
@@ -1,6 +1,6 @@
 swagger: "2.0"
 info:
-  version: "0.50.8-zm4.1"
+  version: "0.50.8-zm4.2"
   title: Gramene API for maizev4
 # basePath prefixes all resource paths
 basePath: /zm4/v50
@@ -219,6 +219,26 @@ paths:
           description: "MongoDB response object"
           schema:
             $ref: "#/definitions/MongoGenetreesResponse"
+  /speciestrees:
+    x-swagger-router-controller: mongo
+    get:
+      summary: "MongoDB"
+      operationId: speciestrees
+      description: "Fetch documents from a collection"
+      parameters:
+        - $ref: "#/parameters/q"
+        - $ref: "#/parameters/rows"
+        - $ref: "#/parameters/start"
+        - $ref: "#/parameters/fl"
+        - $ref: "#/parameters/wt"
+        - $ref: "#/parameters/idList"
+      tags:
+        - "Data access"
+      responses:
+        200:
+          description: "MongoDB response object"
+          schema:
+            $ref: "#/definitions/MongoSpeciestreesResponse"
   /maps:
     x-swagger-router-controller: mongo
     get:
@@ -1013,6 +1033,72 @@ definitions:
       type: integer
       minimum: 0
 
+  MongoSpeciestreesResponse:
+    type: 'array'
+    items:
+      $ref: '#/definitions/SpeciestreeRootNode'
+
+  SpeciestreeRootNode:
+    allOf:
+      - $ref: '#/definitions/SpeciestreeNode'
+      -
+        required:
+          - root_id
+          - compara_db
+        properties:
+          root_id:
+            type: integer
+            minimum: 0
+          compara_db:
+            type: string
+
+  SpeciestreeNode:
+    allOf:
+      - $ref: '#/definitions/SpeciestreeInternalNode'
+      - $ref: '#/definitions/SpeciestreeLeafNode'
+      -
+        required:
+          - node_id
+          - distance_to_parent
+          - left_index
+          - right_index
+          - taxon_id
+          - taxon_name
+          - num_genes
+        properties:
+          node_id:
+            type: integer
+            minimum: 0
+          distance_to_parent:
+            type: number
+            minimum: 0.0
+          left_index:
+            type: integer
+            minimum: 0
+          right_index:
+            type: integer
+          taxon_id:
+            type: integer
+            minimum: 0
+          taxon_name:
+            type: string
+            minimum: 0
+          num_genes:
+            type: integer
+            minimum: 0
+
+  SpeciestreeInternalNode:
+    properties:
+      children:
+        type: array
+        items:
+          $ref: '#/definitions/SpeciestreeNode'
+
+  SpeciestreeLeafNode:
+    properties:
+      system_name:
+        type: string
+
   MongoGenetreesResponse:
     type: 'array'
     items:
@@ -1027,6 +1113,7 @@ definitions:
           - tree_id
           - tree_stable_id
           - tree_type
+          - compara_db
         properties:
           root_id:
             type: integer
@@ -1040,6 +1127,9 @@ definitions:
             enum:
               - 'tree'
               - 'supertree'
+          compara_db:
+            type: string
+
   GenetreeNode:
     allOf:
       - $ref: '#/definitions/GenetreeInternalNode'
diff --git a/npm-shrinkwrap.json b/npm-shrinkwrap.json
index 68ba725..09282ef 100644
--- a/npm-shrinkwrap.json
+++ b/npm-shrinkwrap.json
@@ -23,9 +23,9 @@
       "resolved": "https://registry.npmjs.org/append-field/-/append-field-0.1.0.tgz"
     },
     "argparse": {
-      "version": "1.0.6",
+      "version": "1.0.7",
       "from": "argparse@>=1.0.2 <2.0.0",
-      "resolved": "https://registry.npmjs.org/argparse/-/argparse-1.0.6.tgz"
+      "resolved": "https://registry.npmjs.org/argparse/-/argparse-1.0.7.tgz"
     },
     "array-flatten": {
       "version": "1.1.1",
@@ -445,8 +445,8 @@
     },
     "gramene-mongodb-config": {
       "version": "1.49.0",
-      "from": "warelab/gramene-mongodb-config#zm4",
-      "resolved": "git://github.com/warelab/gramene-mongodb-config.git#532abb1e455381e1ad28b8f1880575c76c601e04"
+      "from": "git://github.com/warelab/gramene-mongodb-config.git#zm4",
+      "resolved": "git://github.com/warelab/gramene-mongodb-config.git#8c8b6a7f530d13455746dd015c9860d53c60be69"
     },
     "har-validator": {
       "version": "2.0.6",
@@ -539,9 +539,9 @@
       "resolved": "https://registry.npmjs.org/js-base64/-/js-base64-2.1.9.tgz"
     },
     "js-yaml": {
-      "version": "3.5.4",
+      "version": "3.5.5",
       "from": "js-yaml@>=3.3.0 <4.0.0",
-      "resolved": "https://registry.npmjs.org/js-yaml/-/js-yaml-3.5.4.tgz"
+      "resolved": "https://registry.npmjs.org/js-yaml/-/js-yaml-3.5.5.tgz"
     },
     "jsbn": {
       "version": "0.1.0",
diff --git a/package.json b/package.json
index 516ceb2..4bc3fbd 100644
--- a/package.json
+++ b/package.json
@@ -12,7 +12,7 @@
     "csv-stringify": "0.0.8",
     "csv2": "^0.1.1",
     "express": "^4.12.3",
-    "gramene-mongodb-config": "warelab/gramene-mongodb-config#zm4",
+    "gramene-mongodb-config": "git://github.com/warelab/gramene-mongodb-config#zm4",
     "gramene-bedify": "1.0.5",
     "isnumber": "^1.0.0",
     "kerberos": "0.0.18",