Add modality raml

api/config.py

@@ -141,6 +141,7 @@ def apply_env_variables(config):
     'file.json',
     'group-new.json',
     'group-update.json',
+    'modality.json',
     'note.json',
     'packfile.json',
     'permission.json',

raml/api.raml

@@ -51,6 +51,7 @@ resourceTypes:
 /gears: !include resources/gears.raml
 /devices: !include resources/devices.raml
 /rules: !include resources/rules.raml
+/modalities: !include resources/modalities.raml
 /groups: !include resources/groups.raml
 /collections: !include resources/collections.raml
 /sessions: !include resources/sessions.raml

raml/examples/input/modality-new.json

@@ -0,0 +1,8 @@
+{
+    "_id": "MR",
+    "classifications": {
+        "Contrast": ["B0", "B1", "T1", "T2", "T2*", "PD", "MT", "ASL", "Perfusion", "Diffusion", "Spectroscopy", "Susceptibility", "Velocity", "Fingerprinting"],
+        "Intent": ["Structural", "Functional", "Localizer", "Shim", "Calibration"],
+        "Features": ["Quantitative", "Multi-Shell", "Multi-Echo", "Multi-Flip", "Multi-Band", "Steady-State", "3D", "Compressed-Sensing", "Eddy-Current-Corrected", "Fieldmap-Corrected", "Gradient-Unwarped", "Motion-Corrected", "Physio-Corrected"]
+    }
+}

raml/examples/input/modality-update.json

@@ -0,0 +1,7 @@
+{
+    "classifications": {
+        "Contrast": ["B0", "B1", "T1", "T2", "T2*", "PD", "MT", "ASL", "Perfusion", "Diffusion", "Spectroscopy", "Susceptibility", "Velocity", "Fingerprinting"],
+        "Intent": ["Structural", "Functional", "Localizer", "Shim", "Calibration"],
+        "Features": ["Quantitative", "Multi-Shell", "Multi-Echo", "Multi-Flip", "Multi-Band", "Steady-State", "3D", "Compressed-Sensing", "Eddy-Current-Corrected", "Fieldmap-Corrected", "Gradient-Unwarped", "Motion-Corrected", "Physio-Corrected"]
+    }
+}

raml/examples/output/modality-list.json

@@ -0,0 +1,10 @@
+[
+	{
+	    "_id": "MR",
+	    "classifications": {
+	        "Contrast": ["B0", "B1", "T1", "T2", "T2*", "PD", "MT", "ASL", "Perfusion", "Diffusion", "Spectroscopy", "Susceptibility", "Velocity", "Fingerprinting"],
+	        "Intent": ["Structural", "Functional", "Localizer", "Shim", "Calibration"],
+	        "Features": ["Quantitative", "Multi-Shell", "Multi-Echo", "Multi-Flip", "Multi-Band", "Steady-State", "3D", "Compressed-Sensing", "Eddy-Current-Corrected", "Fieldmap-Corrected", "Gradient-Unwarped", "Motion-Corrected", "Physio-Corrected"]
+	    }
+	}
+]

raml/examples/output/modality.json

@@ -0,0 +1,8 @@
+{
+    "_id": "MR",
+    "classifications": {
+        "Contrast": ["B0", "B1", "T1", "T2", "T2*", "PD", "MT", "ASL", "Perfusion", "Diffusion", "Spectroscopy", "Susceptibility", "Velocity", "Fingerprinting"],
+        "Intent": ["Structural", "Functional", "Localizer", "Shim", "Calibration"],
+        "Features": ["Quantitative", "Multi-Shell", "Multi-Echo", "Multi-Flip", "Multi-Band", "Steady-State", "3D", "Compressed-Sensing", "Eddy-Current-Corrected", "Fieldmap-Corrected", "Gradient-Unwarped", "Motion-Corrected", "Physio-Corrected"]
+    }
+}

raml/resources/modalities.raml

@@ -0,0 +1,77 @@
+description: Utility functions for modalities and their acceptable classifications.
+get:
+  description: |
+    List all modalities and their classifications.
+    Requires login.
+  responses:
+    200:
+      body:
+        application/json:
+          example: !include ../examples/output/modality-list.json
+          schema: !include ../schemas/output/modality-list.json
+post:
+  description: |
+    Insert a modality type and its classifications map.
+    Requires admin.
+  body:
+    application/json:
+      example: !include ../examples/input/modality-new.json
+      schema: !include ../schemas/input/modality.json
+  responses:
+    200:
+      body:
+        application/json:
+          example: |
+            {
+              "inserted": "1"
+            }
+
+/{ModalityName}:
+  description: Perform actions with a specific modality
+  uriParameters:
+    ModalityName:
+      type: string
+  get:
+    description: |
+      Get modality details.
+      Requires login.
+    responses:
+      200:
+        body:
+          application/json:
+            example: !include ../examples/output/modality.json
+            schema: !include ../schemas/output/modality.json
+      404:
+        description: Modality not found
+  put:
+    description: |
+      Replace a modality's classifications map.
+      Requires admin.
+    body:
+      application/json:
+        example: !include ../examples/input/modality-update.json
+        schema: !include ../schemas/input/modality.json
+    responses:
+      200:
+        body:
+          application/json:
+            example: |
+              {
+                "modified": "1"
+              }
+      404:
+        description: Modality not found
+  delete:
+    description: |
+      Remove a modality.
+      Requires admin.
+    responses:
+      200:
+        body:
+          application/json:
+            example: |
+              {
+                "modified": "1"
+              }
+      404:
+        description: Modality not found

raml/schemas/definitions/modality.json

@@ -0,0 +1,30 @@
+{
+  "$schema": "http://json-schema.org/draft-04/schema#",
+  "type": "object",
+  "definitions": {
+    "_id": {
+      "maxLength": 64,
+      "minLength": 2,
+      "pattern": "^[0-9a-zA-Z_-]*$"
+    },
+    "classifications": {
+      "type": "object",
+      "patternProperties": {
+        "^[0-9a-zA-Z_-]*$":{
+          "type": "array",
+          "items": {
+            "type": "string"
+          }
+        },
+      },
+    },
+    "modality":{
+        "type": "object",
+        "properties": {
+          "_id":                {"$ref":"#/definitions/_id"},
+          "classifications":    {"$ref":"#/definitions/classifications"}
+        },
+        "additionalProperties": false
+    }
+  }
+}

raml/schemas/input/modality.json

@@ -0,0 +1,5 @@
+{
+  "$schema": "http://json-schema.org/draft-04/schema#",
+  "allOf":[{"$ref":"../definitions/modality.json#/definitions/modality"}],
+  "required": ["classifications"]
+}

raml/schemas/output/modality-list.json

@@ -0,0 +1,8 @@
+{
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "type":"array",
+    "items":{
+        "allOf":[{"$ref":"../definitions/modality.json#/definitions/modality"}],
+        "required":["_id", "classifications"]
+    }
+}

raml/schemas/output/modality.json

@@ -0,0 +1,5 @@
+{
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "allOf":[{"$ref":"../definitions/modality.json#/definitions/modality"}],
+    "required": ["_id", "classifications"]
+}

test/integration_tests/abao/abao_test_hooks.js

@@ -23,6 +23,7 @@ var test_project_1 = null;
 var test_project_tag = 'test-project-tag';
 var delete_project_id = '';
 var device_id = 'bootstrapper_Bootstrapper'
+var modality_name = 'MR'
 
 // Tests we're skipping, fix these
 
@@ -1493,3 +1494,53 @@ hooks.before("GET /devices/{DeviceId} -> 404", function(test, done) {
     test.request.params.DeviceId = 'bad_device_id';
     done();
 });
+
+hooks.before("GET /modalities/{ModalityName} -> 200", function(test, done) {
+    test.request.params.ModalityName = modality_name;
+    done();
+});
+
+hooks.before("GET /modalities/{ModalityName} -> 404", function(test, done) {
+    test.request.params.ModalityName = 'bad_modality_name';
+    done();
+});
+
+hooks.before("POST /modalities/ -> 200", function(test, done) {
+    test.request.body = {
+        "_id":"MR",
+        "classifications": {
+            "intent": ["functional"]
+        }
+    }
+    done();
+});
+
+hooks.before("PUT /modalities/{ModalityName} -> 200", function(test, done) {
+    test.request.params.ModalityName = modality_name;
+    test.request.body = {
+        "classifications": {
+            "intent": ["localizer"]
+        }
+    }
+    done();
+});
+
+hooks.before("PUT /modalities/{ModalityName} -> 404", function(test, done) {
+    test.request.params.ModalityName = 'bad_modality_name';
+    test.request.body = {
+        "classifications": {
+            "intent": ["localizer"]
+        }
+    }
+    done();
+});
+
+hooks.before("DELETE /modalities/{ModalityName} -> 200", function(test, done) {
+    test.request.params.ModalityName = modality_name;
+    done();
+});
+
+hooks.before("DELETE /modalities/{ModalityName} -> 404", function(test, done) {
+    test.request.params.ModalityName = 'bad_modality_name';
+    done();
+});