Refactor JSON Schemas and remove ABAO

TESTING.md

@@ -13,7 +13,6 @@ All tests are executed by default. Subsets can be run using the filtering option
 * To run linting, use `--lint` (`-l`)
 * To run unit tests, use `--unit` (`-u`)
 * To run integration tests, use `--integ` (`-i`)
-* To run abao tests, use `--abao` (`-a`)
 * To pass any arguments to `py.test`, use `-- PYTEST_ARGS`
 
 See [py.test usage](https://docs.pytest.org/en/latest/usage.html) for more.
@@ -34,11 +33,3 @@ Without rebuilding the image, run only integration tests matching `foo`, use the
 ```
 
 **NOTE:** The mongodb version is pinned via the `MONGO_VERSION` variable in `tests/bin/run-tests-docker.sh`.
-
-### Tools
-- [abao](https://github.com/cybertk/abao/)
-
-### Testing API against RAML with Abao
-Abao is one of the testing tools run during our TravisCI build.  It tests the API implementation against what’s defined in the RAML spec.  Adding a new resource / url to the RAML spec will cause Abao to verify that resource during integration tests.  Sometimes abao cannot properly test a resource (file field uploads) or a test may require chaining variable.  Abao has before and after hooks for tests, written in javascript.  These can be used to skip a test, inject variables into the request, or make extra assertions about the response.  See tests/integration/abao in the repo for the hooks file.  See [abao github readme](https://github.com/cybertk/abao/blob/master/README.md) for more information on how to use hooks.
-
-Abao tests can depend on specific resources (eg. group, project, session, etc.) pre-existing in the DB. That resource loading should be maintained within `tests/integration_tests/abao/load_fixture.py` and is executed automatically via the integration test scripts at `test/bin`.

api/config.py

@@ -157,7 +157,6 @@ expected_input_schemas = set([
     'avatars.json',
     'collection.json',
     'collection-update.json',
-    'container.json',
     'device.json',
     'file.json',
     'file-update.json',
@@ -182,8 +181,7 @@ expected_input_schemas = set([
     'enginemetadata.json',
     'labelupload.json',
     'uidupload.json',
-    'uidmatchupload.json',
-    'search.json'
+    'uidmatchupload.json'
 ])
 mongo_schemas = set()
 input_schemas = set()

raml/examples/input/acquisition-update.json

-{
-	"label": "example-acquisition-new-label"
-}

raml/examples/input/acquisition.json

-{
-	"label": "example-acquisition",
-	"session": "57e45328466d8e000e33a85b",
-	"public": false
-}

raml/examples/input/analysis-job.json

-{
-    "analysis": {
-        "label": "Test Analysis 1"
-    },
-    "job" : {
-        "gear": "dcm_convert",
-        "inputs": {
-            "dicom": {
-                "type": "acquisition",
-                "id": "57081d06b386a6dc79ca386b",
-                "name" : "test_acquisition_dicom.zip"
-            }
-        },
-        "tags": ["example"]
-    }
-}

raml/examples/input/analysis.json

@@ -43,5 +43,5 @@
 	"description": "This is an analysis description",
 	"job": "54759eb3c090d83494e2d804",
 	"label": "Analysis label",
-	"user": "user_1"
-}
\ No newline at end of file
+    "user": "canakgun@flywheel.io"
+}

raml/examples/input/collection-update.json

-{
-	"contents": {
-		"operation": "add",
-		"nodes": [{
-			"level": "session",
-			"_id": "57dc50b0931cefd8ac2a371e"
-		}]
-	}
-}

raml/examples/input/collection.json

-{"label":"control-group","description":"Control group collection"}

raml/examples/input/device.json

-{
-  "info": {
-    "basic": "info"
-  },
-  "errors": [
-    "An Error"
-  ],
-  "interval": 400
-}

raml/examples/input/group-new.json

-{
-  "label": "Example Group",
-  "_id": "example_group"
-}

raml/examples/input/group-update.json

-{
-    "label":"New group label"
-}

raml/examples/input/note.json

-{
-    "text":"Scitran core!"
-}

raml/examples/input/permission.json

-{
-    "_id":"coltonlw@flywheel.io",
-    "access":"admin"
-}

raml/examples/input/tag.json

-{
-    "value":"example-tag"
-}

raml/examples/input/user-new.json

-{
-	"_id": "jane.doe@gmail.com",
-	"firstname": "Jane",
-	"lastname": "Doe",
-	"email": "jane.doe@gmail.com",
-	"root": false
-}

raml/examples/input/user-update.json

-{
-	"firstname": "Jane",
-	"lastname": "Smith",
-	"email": "jane.smith@gmail.com"
-}

raml/examples/output/job-list.json

 [
     {
-        "inputs": [
-          {
-            "input": "dicom",
-            "type": "acquisition",
-            "id": "57d75ec38e4eb9699b3c245e",
-            "name": "1_1_dicom.zip"
-          }
-        ],
+        "inputs": {
+            "dicom": {
+                "type": "acquisition",
+                "id": "57d75ec38e4eb9699b3c245e",
+                "name": "1_1_dicom.zip"
+            }
+        },
         "attempt": 1,
         "gear_id": "dcm-convert",
         "tags": [
@@ -20,20 +19,19 @@
         "modified": "2016-08-11T12:46:12.593000+00:00",
         "created": "2016-08-11T12:46:12.593000+00:00",
         "state": "pending",
-        "_id": "57ac7394c700190017123fb8",
+        "id": "57ac7394c700190017123fb8",
         "config":{
             "speed":3
         }
     },
     {
-        "inputs": [
-            {
-                "input":"dicom",
+        "inputs": {
+            "dicom": {
                 "type": "acquisition",
                 "id": "57ac7394c700190017123fb7",
                 "name": "8403_4_1_t1_dicom.zip"
             }
-        ],
+        },
         "attempt": 1,
         "gear_id": "dcm_convert",
         "tags": [
@@ -47,7 +45,7 @@
         "modified": "2016-08-11T13:02:09.055000+00:00",
         "created": "2016-08-11T13:02:09.055000+00:00",
         "state": "pending",
-        "_id": "57ac77515e325c0018cd17cf",
+        "id": "57ac77515e325c0018cd17cf",
         "config":{
             "speed":3
         }

raml/examples/output/job-next.json

-{
-	"inputs": [{
-		"input": "dicom",
-		"type": "acquisition",
-		"id": "57e45279a74e91000ed6898f",
-		"name": "4784_1_1_localizer_dicom.zip"
-	}],
-	"attempt": 1,
-	"gear_id": "dicom-mr-classifier",
-	"tags": ["dicom-mr-classifier"],
-	"destination": {
-		"type": "acquisition",
-		"id": "57e45279a74e91000ed6898f"
-	},
-	"request": {
-		"inputs": [{
-			"vu": "vu0:sha384:tXvdI2pspng-YH6lwa2UcLsww0yR6LfEKbLm89eIqEGicLRHW9d1V8bs7gXHTlZ3",
-			"type": "http",
-			"location": "/",
-			"uri": "https://storage.googleapis.com/flywheel/gears/v1/scitran/dicom-mr-classifier/dicom-mr-classifier_latest_20160803T220847.856417Z.tar.gz"
-		}, {
-			"type": "scitran",
-			"uri": "/acquisitions/57e45279a74e91000ed6898f/files/4784_1_1_localizer_dicom.zip",
-			"location": "/flywheel/v0/input/dicom"
-		}],
-		"target": {
-			"command": ["bash", "-c", "rm -rf output; mkdir -p output; ./run; echo \"Exit was $?\""],
-			"env": {
-				"PATH": "/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"
-			},
-			"dir": "/flywheel/v0"
-		},
-		"outputs": [{
-			"type": "scitran",
-			"uri": "/engine?level=acquisition&id=57e45279a74e91000ed6898f&job=57e45279a74e91000ed68991",
-			"location": "/flywheel/v0/output"
-		}]
-	},
-	"modified": "2016-09-28T16:11:36.260000+00:00",
-	"created": "2016-09-22T21:51:53.174000+00:00",
-	"state": "running",
-	"_id": "57e45279a74e91000ed68991",
-	"config": null
-}

raml/schemas/definitions/acquisition.json

@@ -2,11 +2,10 @@
     "$schema": "http://json-schema.org/draft-04/schema#",
     "definitions":{
         "acquisition-input":{
-            "x-gen-name": "acquisition",
             "type": "object",
             "properties": {
                 "public":       {"$ref":"container.json#/definitions/public"},
-                "label":        {"$ref":"container.json#/definitions/label"},
+                "label":        {"$ref":"common.json#/definitions/label"},
                 "info":         {"$ref":"container.json#/definitions/info"},
                 "session":      {"$ref":"common.json#/definitions/objectid"},
                 "uid":          {"$ref":"container.json#/definitions/uid"},
@@ -15,13 +14,32 @@
             },
             "additionalProperties":false
         },
+        "acquisition-metadata-input": {
+            "type": "object",
+            "x-note": "Are all of these fields still used/valid? Can this be reconciled with enginemetadata.json#/definitions/uid-upload-input?",
+            "properties": {
+                "public":       {"type": ["boolean", "null"]},
+                "label":        {"type": ["string", "null"]},
+                "info":         {"type": ["object", "null"]},
+                "metadata":     {"type": ["object", "null"]},
+                "measurement":  {"type": ["string", "null"]},
+                "instrument":   {"type": ["string", "null"]},
+                "uid":          {"type": ["string", "null"]},
+                "timestamp":    {"$ref":"container.json#/definitions/timestamp"},
+                "timezone":     {"type": ["string", "null"]},
+                "files":        {
+                    "type": ["array", "null"],
+                    "items": {"$ref": "file.json#/definitions/file-input"}
+                }
+            },
+            "additionalProperties": false
+        }, 
         "acquisition-output":{
-            "x-gen-name": "acquisition",
             "type":"object",
             "properties": {
               "_id":          {"$ref":"common.json#/definitions/objectid"},
               "public":       {"$ref":"container.json#/definitions/public"},
-              "label":        {"$ref":"container.json#/definitions/label"},
+              "label":        {"$ref":"common.json#/definitions/label"},
               "info":         {"$ref":"container.json#/definitions/info"},
               "session":      {"$ref":"common.json#/definitions/objectid"},
               "uid":          {"$ref":"container.json#/definitions/uid"},

raml/schemas/definitions/analysis.json

@@ -9,17 +9,16 @@
 							"type": ["array", "null"],
 						 	"items": {"$ref":"file.json#/definitions/file"}
 						},
-        "user":     	{"type": "string"},
 		"analysis-input":{
 			"type":"object",
 			"properties":{
 				"inputs":      {"$ref":"#/definitions/inputs"},
 				"outputs":     {"$ref":"#/definitions/outputs"},
 				"notes":       {"$ref":"note.json#/definitions/notes-list-output"},
-				"description": {"type":"string"},
+				"description": {"$ref":"common.json#/definitions/description"},
 				"job":         {"$ref":"common.json#/definitions/objectid"},
 				"label":       {"$ref":"common.json#/definitions/label"},
-				"user":        {"$ref":"#/definitions/user"}
+				"user":        {"$ref":"common.json#/definitions/user-id"}
 			},
 		    "additionalProperties": false
 		},
@@ -45,13 +44,27 @@
 					]
 				},
 				"notes":       {"$ref":"note.json#/definitions/notes-list-output"},
-				"description": {"type":"string"},
+				"description": {"$ref":"common.json#/definitions/description"},
 				"label":       {"$ref":"common.json#/definitions/label"},
 				"user":        {"$ref":"common.json#/definitions/user-id"},
 				"created":     {"$ref":"created-modified.json#/definitions/created"},
 				"modified":    {"$ref":"created-modified.json#/definitions/modified"}
 			},
 			"required":["_id", "files", "label", "user", "created", "modified"]
+		},
+		"analysis-job": {
+			"type": "object",
+				"properties":{
+					"analysis":{
+					"type":"object",
+					"allOf":[{"$ref":"#/definitions/analysis-input"}],
+					"required":["label"]
+				}
+			},
+			"job":{
+				"type":"object",
+				"allOf":[{"$ref":"job.json#/definitions/job-input"}]
+			}
 		}
     }
 }