Add RAML for ContainerHandler based routes

raml/schemas/output/group.json

+{
+  "$schema": "http://json-schema.org/draft-04/schema#",
+  "type": "object",
+  "allOf":[{"ref":"../definitions/group.json#/definitions/group-output"}],
+  "required": [
+         "roles",
+         "created",
+         "modified",
+         "_id"
+       ]
+}

raml/schemas/output/groups-list.json

@@ -2,6 +2,12 @@
   "$schema": "http://json-schema.org/draft-04/schema#",
   "type": "array",
   "items": {
-    "$ref":"../definitions/group-output.json#"
+    "allOf":[{"ref":"../definitions/group.json#/definitions/group-output"}],
+    "required": [
+           "roles",
+           "created",
+           "modified",
+           "_id"
+         ]
   }
 }

raml/schemas/output/job-list.json

@@ -2,14 +2,23 @@
   "$schema": "http://json-schema.org/draft-04/schema#",
   "type": "array",
   "items": {
-    "allOf":[
-      {"$ref":"../definitions/job-output.json#"},
-      {
-        "required":[
-           "_id", "name", "inputs",
-           "destination", "tags", "state", "attempt"
-           ]
-      }
+    "type":"object",
+    "properties":{
+      "_id":{"$ref":"../definitions/job.json#/definitions/id"},
+      "name":{"$ref":"../definitions/job.json#/definitions/name"},
+      "inputs":{"$ref":"../definitions/job.json#/definitions/inputs-array"},
+      "destination":{"$ref":"../definitions/job.json#/definitions/destination"},
+      "tags":{"$ref":"../definitions/job.json#/definitions/tags"},
+      "state":{"$ref":"../definitions/job.json#/definitions/state"},
+      "attempt":{"$ref":"../definitions/job.json#/definitions/attempt"},
+      "created":{"$ref":"../definitions/created-modified.json#/definitions/created"},
+      "modified":{"$ref":"../definitions/created-modified.json#/definitions/modified"},
+      "config":{"$ref":"../definitions/job.json#/definitions/config"}
+    },
+    "additionalProperties":false,
+    "required":[
+       "_id", "name", "inputs",
+       "destination", "tags", "state", "attempt"
     ]
   }
 }

raml/schemas/output/job-next.json

+{
+  "$schema": "http://json-schema.org/draft-04/schema#",
+  "type":"object",
+  "properties":{
+    "_id":{"$ref":"../definitions/job.json#/definitions/id"},
+    "name":{"$ref":"../definitions/job.json#/definitions/name"},
+    "inputs":{"$ref":"../definitions/job.json#/definitions/inputs-array"},
+    "destination":{"$ref":"../definitions/job.json#/definitions/destination"},
+    "tags":{"$ref":"../definitions/job.json#/definitions/tags"},
+    "state":{"$ref":"../definitions/job.json#/definitions/state"},
+    "attempt":{"$ref":"../definitions/job.json#/definitions/attempt"},
+    "created":{"$ref":"../definitions/created-modified.json#/definitions/created"},
+    "modified":{"$ref":"../definitions/created-modified.json#/definitions/modified"},
+    "config":{"$ref":"../definitions/job.json#/definitions/config"},
+    "request":{"$ref":"../definitions/job.json#/definitions/request"}
+  },
+  "additionalProperties":false,
+  "required":[
+     "_id", "name", "inputs", "config",
+     "destination", "tags", "state", "attempt"
+  ]
+}

raml/schemas/output/job.json

 {
   "$schema": "http://json-schema.org/draft-04/schema#",
-  "allOf":[
-    {"$ref":"../definitions/job.json#"},
-    {"$ref":"../definitions/created-modified.json#"},
-    {
-      "type":"object",
-      "properties":{
-        "id":{"type":"string"},
-        "name":{},
-        "inputs":{},
-        "destination":{},
-        "origin": {},
-        "saved_files": {},
-        "tags":{},
-        "state":{},
-        "attempt":{},
-        "created":{},
-        "modified":{},
-        "config":{
-          "oneOf":[
-            {
-              "enum":[null]
-            },
-            {
-              "type":"object"
-            }
-          ]
-        }
-      },
-      "additionalProperties":false
-    }
-  ],
+  "type":"object",
+  "properties":{
+    "id":{"$ref":"../definitions/job.json#/definitions/id"},
+    "name":{"$ref":"../definitions/job.json#/definitions/name"},
+    "inputs":{"$ref":"../definitions/job.json#/definitions/inputs-object"},
+    "destination":{"$ref":"../definitions/job.json#/definitions/destination"},
+    "tags":{"$ref":"../definitions/job.json#/definitions/tags"},
+    "state":{"$ref":"../definitions/job.json#/definitions/state"},
+    "attempt":{"$ref":"../definitions/job.json#/definitions/attempt"},
+    "created":{"$ref":"../definitions/created-modified.json#/definitions/created"},
+    "modified":{"$ref":"../definitions/created-modified.json#/definitions/modified"},
+    "config":{"$ref":"../definitions/job.json#/definitions/config"},
+    "request":{"$ref":"../definitions/job.json#/definitions/request"},
+    "saved_files":{"$ref":"../definitions/job.json#/definitions/saved_files"}
+  },
+  "additionalProperties":false,
   "required":[
      "id", "name", "inputs", "config",
      "destination", "tags", "state", "attempt",

raml/schemas/output/project-list.json

+{
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "type":"array",
+    "items":{
+        "type": "object",
+        "allOf": [{"$ref": "../definitions/project.json#/definitions/project-output"}],
+        "required": [
+            "_id", "label", "group",
+            "created", "modified", "permissions"
+        ]
+    }
+}

raml/schemas/output/project.json

+{
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "Project",
+    "type": "object",
+    "allOf": [{"$ref": "../definitions/project.json#/definitions/project-output"}],
+    "required": [
+        "_id", "label", "group",
+        "created", "modified", "permissions"
+    ]
+}

raml/schemas/output/session-jobs.json

+{
+  "$schema": "http://json-schema.org/draft-04/schema#",
+  "type": "object",
+  "patternProperties": {
+    "^[a-fA-F0-9]{24}$":{
+      "type":"array",
+      "items":{
+        "type":"object",
+        "properties":{
+          "id":{"$ref":"../definitions/job.json#/definitions/id"},
+          "name":{"$ref":"../definitions/job.json#/definitions/name"},
+          "inputs":{"$ref":"../definitions/job.json#/definitions/inputs-object"},
+          "destination":{"$ref":"../definitions/job.json#/definitions/destination"},
+          "tags":{"$ref":"../definitions/job.json#/definitions/tags"},
+          "state":{"$ref":"../definitions/job.json#/definitions/state"},
+          "attempt":{"$ref":"../definitions/job.json#/definitions/attempt"},
+          "created":{"$ref":"../definitions/created-modified.json#/definitions/created"},
+          "modified":{"$ref":"../definitions/created-modified.json#/definitions/modified"},
+          "config":{"$ref":"../definitions/job.json#/definitions/config"},
+          "request":{"$ref":"../definitions/job.json#/definitions/request"}
+        },
+        "additionalProperties":false,
+        "required":[
+           "id", "name", "inputs", "config",
+           "destination", "tags", "state", "attempt"
+        ]
+      }
+    }
+  },
+  "additionalProperties":false
+}

raml/schemas/output/session-list.json

+{
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "type":"array",
+    "items":{
+        "allOf":[{"$ref":"../definitions/session.json#/definitions/session-output"}],
+        "required":[
+            "_id", "label", "project", "created", "modified", "permissions",
+            "public", "group", "subject"
+        ]
+    }
+}

raml/schemas/output/session.json

+{
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "type":"object",
+    "allOf":[{"$ref":"../definitions/session.json#/definitions/session-output"}],
+    "required":[
+        "_id", "label", "project", "created", "modified", "permissions",
+        "public", "group", "subject"
+    ]
+}

raml/schemas/output/user-list.json

@@ -3,13 +3,11 @@
   "type": "array",
   "items": {
     "allOf":[
-      {"$ref":"../definitions/user-output.json#"},
-      {
-        "required":[
-           "_id", "firstname", "lastname",
-           "root", "email", "created", "modified"
-           ]
-      }
+      {"$ref":"../definitions/user.json#/definitions/user-output"}
+    ],
+    "required":[
+       "_id", "firstname", "lastname",
+       "root", "email", "created", "modified"
     ]
   }
 }

raml/schemas/output/user-self.json

 {
   "$schema": "http://json-schema.org/draft-04/schema#",
-  "allOf":[
-    {"$ref":"../definitions/user.json#"},
-    {"$ref":"../definitions/created-modified.json"},
-    {
-      "type":"object",
-      "properties":{
-        "_id":{},
-        "firstname":{},
-        "lastname":{},
-        "email":{},
-        "avatars":{},
-        "root":{},
-        "disabled":{},
-        "preferences":{},
-        "created":{},
-        "modified":{},
-        "api_key": {"$ref":"../definitions/user-api_key.json"}
-      },
-      "additionalProperties":false,
-      "required":[
-         "_id", "firstname", "lastname",
-         "root", "email", "created", "modified"
-         ]
-    }
+  "type":"object",
+  "properties":{
+    "_id":{"$ref":"../definitions/user.json#/definitions/_id"},
+    "firstname":{"$ref":"../definitions/user.json#/definitions/firstname"},
+    "lastname":{"$ref":"../definitions/user.json#/definitions/lastname"},
+    "email":{"$ref":"../definitions/user.json#/definitions/email"},
+    "avatar":{"$ref":"../definitions/user.json#/definitions/avatar"},
+    "avatars":{"$ref":"../definitions/user.json#/definitions/avatars"},
+    "root":{"$ref":"../definitions/user.json#/definitions/root"},
+    "disabled":{"$ref":"../definitions/user.json#/definitions/disabled"},
+    "preferences":{"$ref":"../definitions/user.json#/definitions/preferences"},
+    "created":{"$ref":"../definitions/created-modified.json#/definitions/created"},
+    "modified":{"$ref":"../definitions/created-modified.json#/definitions/modified"},
+    "api_key":{"$ref":"../definitions/user.json#/definitions/api_key"}
+  },
+  "additionalProperties":false,
+  "required":[
+     "_id", "firstname", "lastname",
+     "root", "email", "created", "modified"
   ]
 }

raml/schemas/output/user.json

@@ -2,7 +2,7 @@
   "$schema": "http://json-schema.org/draft-04/schema#",
   "type": "object",
   "allOf":[
-    {"$ref":"../definitions/user-output.json#"},
+    {"$ref":"../definitions/user.json#/definitions/user-output"},
     {
       "required":[
          "_id", "firstname", "lastname",

test/bin/run-integration-tests.sh

@@ -52,10 +52,17 @@ BASE_URL="$SCITRAN_SITE_API_URL" \
     MONGO_PATH="$MONGODB_URI" \
     py.test test/integration_tests/python
 
+PATH=$(npm bin):$PATH
+
+# Allow us to require modules from package.json,
+# since abao_test_hooks.js is not being called from the package directory
+integration_test_node_modules="$( pwd )/node_modules/scitran-core-integration-tests/node_modules"
+
 newman run test/integration_tests/postman/integration_tests.postman_collection -e test/integration_tests/postman/environments/integration_tests.postman_environment
 
 # Have to change into definitions directory to resolve
 # relative $ref's in the jsonschema's
 pushd raml/schemas/definitions
-abao ../../api.raml "--server=$SCITRAN_SITE_API_URL" "--hookfiles=../../../test/integration_tests/abao/abao_test_hooks.js"
+# NODE_PATH="$integration_test_node_modules"
+NODE_PATH="$integration_test_node_modules" abao ../../api.raml "--server=$SCITRAN_SITE_API_URL" "--hookfiles=../../../test/integration_tests/abao/abao_test_hooks.js"
 popd

test/bin/setup-integration-tests-ubuntu.sh

@@ -9,8 +9,8 @@ NODE_URL="https://nodejs.org/dist/v6.4.0/node-v6.4.0-linux-x64.tar.gz"
 
 if [ -z "$VIRTUAL_ENV" ]; then
     curl $NODE_URL | sudo tar xz -C /usr/local --strip-components 1
-    sudo npm install -g test/integration_tests
+    npm install test/integration_tests
 else
     curl $NODE_URL | tar xz -C $VIRTUAL_ENV --strip-components 1
-    npm install -g test/integration_tests
+    npm install test/integration_tests
 fi

test/integration_tests/abao/abao_test_hooks.js

 var hooks = require('hooks');
+var chai = require("chai");
+var assert = chai.assert;
 
 // Variables for passing results as input to subsequent tests
 var job_id = '';
 var gear_name = 'test-case-gear';
 var group_id = 'test_group';
+var collection_id = '';
+var delete_collection_id = '';
+var test_session_1 = null;
+var test_session_2_id = null;
+var test_acquisition_1 = null;
+var test_project_1 = null;
 
 // Tests we're skipping, fix these
 
 // Fails only in travis
 hooks.skip("GET /version -> 200");
 
-// Skipped due to 500 when should 4xx
-
 // Should 400 to say invalid json
 hooks.skip("GET /download -> 400");
 
@@ -23,10 +29,6 @@ hooks.skip("POST /upload/uid-match -> 402");
 // Should 404
 hooks.skip("GET /jobs/{JobId} -> 404");
 
-// This does run after a job is added
-// 500 saying unknown gear
-hooks.skip("GET /jobs/next -> 200");
-
 // Can only retry a failed job
 hooks.skip("POST /jobs/{JobId}/retry -> 200");
 
@@ -34,7 +36,9 @@ hooks.skip("POST /jobs/{JobId}/retry -> 200");
 hooks.skip("GET /users/self/avatar -> 307");
 hooks.skip("GET /users/{UserId}/avatar -> 307");
 
-// Skipping some tests until we figure out how to test file fields
+// Tests that are skipped because we do them in postman or python
+
+// Skipping because abao doesn't support file fields
 hooks.skip("POST /download -> 200");
 hooks.skip("GET /download -> 200");
 hooks.skip("POST /upload/label -> 200");
@@ -193,3 +197,161 @@ hooks.before("DELETE /groups/{GroupId} -> 200", function(test, done) {
     };
     done();
 });
+
+hooks.after("GET /collections -> 200", function(test, done) {
+    collection_id = test.response.body[0]._id;
+    delete_collection_id = test.response.body[1]._id;
+    done();
+});
+
+hooks.before("GET /collections/{CollectionId} -> 200", function(test, done) {
+    test.request.params.CollectionId = collection_id;
+    done();
+});
+
+hooks.before("GET /collections/{CollectionId}/sessions -> 200", function(test, done) {
+    test.request.params.CollectionId = collection_id;
+    done();
+});
+
+hooks.before("GET /collections/{CollectionId}/acquisitions -> 200", function(test, done) {
+    test.request.params.CollectionId = collection_id;
+    done();
+});
+
+hooks.before("POST /collections -> 400", function(test, done) {
+    test.request.params.CollectionId = collection_id;
+    test.request.body.foo = "not an allowed property";
+    done();
+});
+
+hooks.before("PUT /collections/{CollectionId} -> 400", function(test, done) {
+    test.request.params.CollectionId = collection_id;
+    test.request.body.foo = "not an allowed property";
+    done();
+});
+
+hooks.before("DELETE /collections/{CollectionId} -> 200", function(test, done) {
+    test.request.params.CollectionId = delete_collection_id;
+    done();
+});
+
+hooks.after("GET /sessions -> 200", function(test, done) {
+    test_session_1 = test.response.body[0];
+    assert.equal(test_session_1.label, "test-session-1");
+    done();
+});
+
+hooks.before("GET /sessions/{SessionId} -> 200", function(test, done) {
+    test.request.params.SessionId = test_session_1._id;
+    done();
+});
+
+hooks.before("POST /sessions -> 200", function(test, done) {
+    test.request.body.project = test_session_1.project;
+    done();
+});
+
+hooks.after("POST /sessions -> 200", function(test, done) {
+    test_session_2_id = test.response.body._id
+    done();
+});
+
+
+hooks.before("POST /sessions -> 400", function(test, done) {
+    test.request.body.foo = "not an allowed property";
+    test.request.body.project = test_session_1.project;
+    done();
+});
+
+hooks.before("PUT /sessions/{SessionId} -> 200", function(test, done) {
+    test.request.params.SessionId = test_session_1._id;
+    test.request.body = {
+        project: test_session_1.project,
+        label: "new-label-test-session-1"
+    };
+    done();
+});
+
+hooks.before("PUT /sessions/{SessionId} -> 400", function(test, done) {
+    test.request.params.SessionId = test_session_1._id;
+    test.request.body = {
+        project: test_session_1.project,
+        "not_a_real_property": "new-label-test-session-1"
+    };
+    done();
+});
+
+hooks.before("DELETE /sessions/{SessionId} -> 200", function(test, done) {
+    test.request.params.SessionId = test_session_2_id;
+    done();
+});
+
+
+hooks.before("GET /sessions/{SessionId}/jobs -> 200", function(test, done) {
+  test.request.params.SessionId = test_session_1._id;
+  done();
+});
+
+hooks.after("GET /acquisitions -> 200", function(test, done) {
+    test_acquisition_1 = test.response.body[0];
+    assert.equal(test_acquisition_1.label, "test-acquisition-1");
+    example_acquisition = test.response.body[1];
+    done();
+});
+
+hooks.before("GET /acquisitions/{AcquisitionId} -> 200", function(test, done) {
+    test.request.params.AcquisitionId = test_acquisition_1._id;
+    done();
+});
+
+hooks.before("POST /acquisitions -> 200", function(test, done) {
+    test.request.body.session = test_session_1._id;
+    done();
+});
+
+hooks.before("POST /acquisitions -> 400", function(test, done) {
+    test.request.body.session = test_session_1._id;
+    test.request.body.foo = "bar";
+    done();
+});
+
+hooks.before("PUT /acquisitions/{AcquisitionId} -> 200", function(test, done) {
+    test.request.params.AcquisitionId = test_acquisition_1._id;
+    test.request.body = {"label":"test-acquisition-1-new-label"};
+    done();
+});
+
+
+hooks.before("PUT /acquisitions/{AcquisitionId} -> 400", function(test, done) {
+    test.request.params.AcquisitionId = test_acquisition_1._id;
+    test.request.body = {"not-real":"an invalid property"};
+    done();
+});
+
+hooks.before("DELETE /acquisitions/{AcquisitionId} -> 200", function(test, done) {
+    test.request.params.AcquisitionId = example_acquisition._id;
+    done();
+});
+
+hooks.after("GET /projects -> 200", function(test, done) {
+    test_project_1 = test.response.body[0];
+    assert.equal(test_project_1.label, "test-project");
+    done();
+});
+
+hooks.before("POST /projects -> 400", function(test, done) {
+    test.request.body.not_real = "an invalid property";
+    done();
+});
+
+hooks.before("GET /projects/{ProjectId} -> 200", function(test, done) {
+    test.request.params.ProjectId = test_project_1._id;
+    done();
+});
+
+hooks.before("PUT /projects/{ProjectId} -> 400", function(test, done) {
+    test.request.params.ProjectId = test_project_1._id;
+    test.request.body = {"not_real":"fake property"};
+    done();
+});

test/integration_tests/package.json

@@ -4,7 +4,8 @@
   "description": "SciTran Core integation test node dependencies",
   "dependencies": {
     "newman":"3.1.0",
-    "abao":"git+https://github.com/flywheel-io/abao.git#better-jsonschema-ref"
+    "abao":"git+https://github.com/flywheel-io/abao.git#better-jsonschema-ref",
+    "chai": "~3.5.0"
   },
   "bin":{
     "abao":"node_modules/.bin/abao",

test/integration_tests/postman/integration_tests.postman_collection

@@ -356,6 +356,93 @@
 			},
 			"response": []
 		},
+		{
+			"name": "Create test-collection-1",
+			"event": [
+				{
+					"listen": "test",
+					"script": {
+						"type": "text/javascript",
+						"exec": "tests[\"Status code is 200\"] = responseCode.code === 200;\n\ntests[\"Response time is less than 200ms\"] = responseTime < 200;\n\nvar jsonData = JSON.parse(responseBody);\n\npostman.setGlobalVariable(\"test-collection-id\", jsonData._id);"
+					}
+				}
+			],
+			"request": {
+				"url": "{{baseUri}}/collections",
+				"method": "POST",
+				"header": [
+					{
+						"key": "Authorization",
+						"value": "scitran-user {{test_user_api_key}}",
+						"description": ""
+					}
+				],
+				"body": {
+					"mode": "raw",
+					"raw": "{\n    \"label\":\"test-collection-1\"\n}"
+				},
+				"description": ""
+			},
+			"response": []
+		},
+		{
+			"name": "Add test-session-1 to test-collection-1",
+			"event": [
+				{
+					"listen": "test",
+					"script": {
+						"type": "text/javascript",
+						"exec": "tests[\"Status code is 200\"] = responseCode.code === 200;\n\ntests[\"Response time is less than 200ms\"] = responseTime < 200;"
+					}
+				}
+			],
+			"request": {
+				"url": "{{baseUri}}/collections/{{test-collection-id}}",
+				"method": "PUT",
+				"header": [
+					{
+						"key": "Authorization",
+						"value": "scitran-user {{test_user_api_key}}",
+						"description": ""
+					}
+				],
+				"body": {
+					"mode": "raw",
+					"raw": "{\n    \"contents\":{\n    \t\"operation\":\"add\",\n    \t\"nodes\":[\n    \t\t{\n    \t\t\t\"level\":\"session\",\n    \t\t\t\"_id\":\"{{test-session-id}}\"\n    \t\t}\n    \t]\n    }\n}"
+				},
+				"description": ""
+			},
+			"response": []
+		},
+		{
+			"name": "Create test-collection-2",
+			"event": [
+				{
+					"listen": "test",
+					"script": {
+						"type": "text/javascript",
+						"exec": "tests[\"Status code is 200\"] = responseCode.code === 200;\n\ntests[\"Response time is less than 200ms\"] = responseTime < 200;"
+					}
+				}
+			],
+			"request": {
+				"url": "{{baseUri}}/collections",
+				"method": "POST",
+				"header": [
+					{
+						"key": "Authorization",
+						"value": "scitran-user {{test_user_api_key}}",
+						"description": ""
+					}
+				],
+				"body": {
+					"mode": "raw",
+					"raw": "{\n    \"label\":\"test-collection-2\"\n}"
+				},
+				"description": ""
+			},
+			"response": []
+		},
 		{
 			"name": "[Session Template] Create project",
 			"event": [
@@ -734,4 +821,4 @@
 			"response": []
 		}
 	]
-}
\ No newline at end of file
+}