Add RAML for container based routes

scitran · Oct 10, 2016 · 450b27f · 450b27f
1 parent a49aaa3
commit 450b27f
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Showing 35 changed files with 550 additions and 115 deletions.
diff --git a/.gitignore b/.gitignore
@@ -8,3 +8,4 @@ bootstrap.json
 .cache
 /.coverage*
 coverage.xml
+node_modules/
diff --git a/api/api.py b/api/api.py
@@ -145,7 +145,7 @@ def _format(route):
     webapp2.Route(_format(r'/api/<cont_name:{cont_name_re}>'),                          containerhandler.ContainerHandler, name='cont_list', handler_method='get_all', methods=['GET']),
     webapp2.Route(_format(r'/api/<cont_name:{cont_name_re}>'),                          containerhandler.ContainerHandler, methods=['POST']),
     webapp2.Route(_format(r'/api/<cont_name:{cont_name_re}>/<cid:{cid_re}>'),           containerhandler.ContainerHandler, name='cont_details', methods=['GET','PUT','DELETE']),
-    webapp2.Route(_format(r'/api/<cont_name:{cont_name_re}>/<cid:{cid_re}>/jobs'),           containerhandler.ContainerHandler, name='cont_jobs', handler_method='get_jobs', methods=['GET']),
+    webapp2.Route(_format(r'/api/sessions/<cid:{cid_re}>/jobs'),           containerhandler.ContainerHandler, name='cont_jobs', handler_method='get_jobs', methods=['GET']),
 
     webapp2.Route(_format(r'/api/<cont_name:groups>/<cid:{group_id_re}>/<list_name:roles>'),                                        listhandler.ListHandler, name='group_roles_post'),
     webapp2.Route(_format(r'/api/<cont_name:groups>/<cid:{group_id_re}>/<list_name:roles>/<site:{site_id_re}>/<_id:{user_id_re}>'),    listhandler.ListHandler, name='group_roles', methods=['GET', 'PUT', 'DELETE']),

diff --git a/api/config.py b/api/config.py
@@ -118,6 +118,7 @@ def apply_env_variables(config):
 ])
 expected_input_schemas = set([
     'acquisition.json',
+    'acquisition-update.json',
     'analysis.json',
     'avatars.json',
     'collection.json',
@@ -130,6 +131,7 @@ def apply_env_variables(config):
     'packfile.json',
     'permission.json',
     'project.json',
+    'project-update.json',
     'session.json',
     'session-update.json',
     'subject.json',

diff --git a/api/handlers/containerhandler.py b/api/handlers/containerhandler.py
@@ -172,63 +172,10 @@ def _filter_permissions(self, result, uid, site):
         if user_perm.get('access') != 'admin':
             result['permissions'] = [user_perm] if user_perm else []
 
-    def get_jobs(self, cont_name, cid):
-        """
-        .. http:get:: /api/(cont_name)/(cid)/jobs
-
-            Return any jobs that mention this container as an input.
-
-            :query states: filter results by job state
-            :type states: string
-
-            :query tags: filter results by job tags
-            :type cid: string
-
-            :statuscode 200: no error
-
-            **Example request**:
-
-            .. sourcecode:: http
-
-                GET /api/sessions/3/jobs?states=pending&states=failed&tags=a&tags=b HTTP/1.1
-                Host: demo.flywheel.io
-                Accept: */*
-
-
-            **Example response**:
-
-            .. sourcecode:: http
-
-                HTTP/1.1 200 OK
-                Vary: Accept-Encoding
-                Content-Type: application/json; charset=utf-8
-                [
-                    {
-                        "_id": "57336257ea360500272c2f11",
-                        "algorithm_id": "dicom_mr_classifier",
-                        "state": "pending",
-                        "tags": [
-                            "a"
-                        ]
-                        //...
-                    },
-                    {
-                        "_id": "57336257ea360500272c2f12",
-                        "algorithm_id": "dcm_convert",
-                        "state": "failed",
-                        "tags": [
-                            "b"
-                        ]
-                       // ...
-                    }
-                ]
-        """
-
-        self.config = self.container_handler_configurations[cont_name]
+    def get_jobs(self, cid):
+        # Only enabled for sessions container type per url rule in api.py
+        self.config = self.container_handler_configurations["sessions"]
         self.storage = self.config['storage']
-        if cont_name != 'sessions':
-            self.abort(400, 'Can only request jobs at the session level.')
-
         cont = self._get_container(cid, projection={'permissions': 0}, get_children=True)
         permchecker = self._get_permchecker(cont)
         permchecker(noop)('GET', cid)

diff --git a/bin/install-dev-osx.sh b/bin/install-dev-osx.sh
@@ -87,4 +87,4 @@ fi
 # Install testing dependencies
 echo "Installing testing dependencies"
 pip install -r "test/integration_tests/requirements-integration-test.txt"
-npm install -g test/integration_tests
+npm install test/integration_tests
diff --git a/raml/api.raml b/raml/api.raml
@@ -32,3 +32,5 @@ resourceTypes:
 /groups: !include resources/groups.raml
 /collections: !include resources/collections.raml
 /sessions: !include resources/sessions.raml
+/acquisitions: !include resources/acquisitions.raml
+/projects: !include resources/projects.raml
diff --git a/raml/examples/input/acquisition-update.json b/raml/examples/input/acquisition-update.json
@@ -0,0 +1,3 @@
+{
+	"label": "example-acquisition-new-label"
+}
diff --git a/raml/examples/input/acquisition.json b/raml/examples/input/acquisition.json
@@ -0,0 +1,5 @@
+{
+	"label": "example-acquisition",
+	"session": "57e45328466d8e000e33a85b",
+	"public": false
+}
diff --git a/raml/examples/input/project-update.json b/raml/examples/input/project-update.json
@@ -0,0 +1 @@
+{"label":"test2-project-new-label"}
diff --git a/raml/examples/input/project.json b/raml/examples/input/project.json
@@ -0,0 +1 @@
+{"group":"scitran","label":"test2"}
diff --git a/raml/examples/output/acquisition.json b/raml/examples/output/acquisition.json
@@ -0,0 +1,40 @@
+{
+  "files": [
+    {
+      "origin": {
+        "method": "importer",
+        "type": "device",
+        "id": "importer_Admin_Import",
+        "name": "Admin Import"
+      },
+      "mimetype": "application/zip",
+      "measurements": [],
+      "hash": "v0-sha384-dd3c97bfe0ad1fcba75ae6718c6e81038c59af4f447f5db194d52732efa4f955b28455db02eb64cad3e4e55f11e3679f",
+      "name": "4784_1_1_localizer_dicom.zip",
+      "tags": [],
+      "created": "2016-09-21T14:56:09.943000+00:00",
+      "modified": "2016-09-21T14:56:09.943000+00:00",
+      "instrument": null,
+      "metadata": {},
+      "type": "dicom",
+      "size": 989933
+    }
+  ],
+  "created": "2016-09-21T14:56:10.026000+00:00",
+  "timestamp": "2016-09-21T19:24:45.539570+00:00",
+  "modified": "2016-09-21T14:56:10.026000+00:00",
+  "label": "4784_1_1_localizer",
+  "session": "57e29f8afab726000f7ec6b1",
+  "collections": [
+    "57e2a026675ca0000f0eeb0c"
+  ],
+  "_id": "57e29f8afab726000f7ec6b2",
+  "public": false,
+  "permissions": [
+    {
+      "access": "admin",
+      "_id": "coltonlw@flywheel.io",
+      "site": "local"
+    }
+  ]
+}
diff --git a/raml/examples/output/job-next.json b/raml/examples/output/job-next.json
@@ -1,27 +1,44 @@
 {
-  "inputs": [
-    {
-      "input": "dicom",
-      "type": "acquisition",
-      "id": "57e45279a74e91000ed6898f",
-      "name": "4784_1_1_localizer_dicom.zip"
-    }
-  ],
-  "attempt": 1,
-  "name": "dcm_convert",
-  "tags": [
-    "ad-hoc",
-    "dcm_convert"
-  ],
-  "destination": {
-    "type": "acquisition",
-    "id": "573c9e6a844eac7fc01747cd"
-  },
-  "modified": "2016-08-11T13:02:09.055000+00:00",
-  "created": "2016-08-11T13:02:09.055000+00:00",
-  "state": "pending",
-  "_id": "57ac77515e325c0018cd17cf",
-  "config":{
-    "speed":3
-  }
+	"inputs": [{
+		"input": "dicom",
+		"type": "acquisition",
+		"id": "57e45279a74e91000ed6898f",
+		"name": "4784_1_1_localizer_dicom.zip"
+	}],
+	"attempt": 1,
+	"name": "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
 }
diff --git a/raml/examples/output/project-list.json b/raml/examples/output/project-list.json
@@ -0,0 +1,60 @@
+[{
+	"group": "scitran",
+	"created": "2016-09-22T21:51:53.151000+00:00",
+	"modified": "2016-09-22T21:51:53.151000+00:00",
+	"label": "Neuroscience",
+	"_id": "57e452791cff88b85f9f9c97",
+	"public": false,
+	"permissions": [{
+		"access": "admin",
+		"_id": "coltonlw@flywheel.io",
+		"site": "local"
+	}]
+}, {
+	"group": "scitran",
+	"created": "2016-09-22T21:52:27.576000+00:00",
+	"modified": "2016-09-22T21:52:27.576000+00:00",
+	"label": "Psychology",
+	"_id": "57e4529b1cff88b85f9f9c98",
+	"public": false,
+	"permissions": [{
+		"access": "admin",
+		"_id": "coltonlw@flywheel.io",
+		"site": "local"
+	}]
+}, {
+	"group": "scitran",
+	"created": "2016-09-22T21:52:52.539000+00:00",
+	"modified": "2016-09-22T21:52:52.539000+00:00",
+	"label": "Testdata",
+	"_id": "57e452b41cff88b85f9f9c99",
+	"public": false,
+	"permissions": [{
+		"access": "admin",
+		"_id": "coltonlw@flywheel.io",
+		"site": "local"
+	}]
+}, {
+	"group": "test-group",
+	"created": "2016-09-22T21:54:47.925000+00:00",
+	"modified": "2016-09-22T21:54:47.925000+00:00",
+	"label": "test-project",
+	"_id": "57e45327466d8e000e33a859",
+	"public": false,
+	"permissions": [{
+		"access": "admin",
+		"_id": "coltonlw@flywheel.io",
+		"site": "local"
+	}]
+}, {
+	"group": "scitran",
+	"created": "2016-09-29T18:53:06.199000+00:00",
+	"modified": "2016-09-29T18:53:06.199000+00:00",
+	"label": "test2",
+	"_id": "57ed6312466d8e01c91ee427",
+	"permissions": [{
+		"access": "admin",
+		"_id": "coltonlw@flywheel.io",
+		"site": "local"
+	}]
+}]
diff --git a/raml/examples/output/project.json b/raml/examples/output/project.json
@@ -0,0 +1,13 @@
+{
+	"group": "scitran",
+	"created": "2016-09-22T21:51:53.151000+00:00",
+	"modified": "2016-09-22T21:51:53.151000+00:00",
+	"label": "Neuroscience",
+	"_id": "57e452791cff88b85f9f9c97",
+	"public": false,
+	"permissions": [{
+		"access": "admin",
+		"_id": "coltonlw@flywheel.io",
+		"site": "local"
+	}]
+}
diff --git a/raml/examples/output/session-jobs.json b/raml/examples/output/session-jobs.json
@@ -0,0 +1,60 @@
+{
+    "57ebe5adf0a2c90027d2bd44": [
+        {
+            "inputs": {
+                "dicom": {
+                    "type": "acquisition",
+                    "id": "57ebe5adf0a2c90027d2bd44",
+                    "name": "1_1_dicom.zip"
+                }
+            },
+            "attempt": 1,
+            "name": "dcm_convert",
+            "tags": [
+                "dcm_convert",
+                "spectroscopy"
+            ],
+            "destination": {
+                "type": "acquisition",
+                "id": "57ebe5adf0a2c90027d2bd44"
+            },
+            "request": {
+                "inputs": [
+                    {
+                        "type": "scitran",
+                        "uri": "/jobs/57ebe5adf0a2c90027d2bd48/config.json",
+                        "location": "/flywheel/v0"
+                    },
+                    {
+                        "type": "scitran",
+                        "uri": "/acquisitions/57ebe5adf0a2c90027d2bd44/files/1_1_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=57ebe5adf0a2c90027d2bd44&job=57ebe5adf0a2c90027d2bd48",
+                        "location": "/flywheel/v0/output"
+                    }
+                ]
+            },
+            "modified": "2016-09-28T15:45:52.607000+00:00",
+            "created": "2016-09-28T15:45:49.975000+00:00",
+            "state": "running",
+            "config": {},
+            "id": "57ebe5adf0a2c90027d2bd48"
+        }
+    ]
+}
diff --git a/raml/resourceTypes/container-item.raml b/raml/resourceTypes/container-item.raml
@@ -1,4 +1,3 @@
-description: Entity representing a <<resourcePathName|!singularize>>
 get:
   description: Get a single <<resourcePathName|!singularize>>
   responses: