Merge pull request #592 from scitran/api-spec-listhandler-2

Add RAML for listhandler and other remaining endpoints

api/config.py

@@ -120,6 +120,7 @@ expected_input_schemas = set([
     'acquisition.json',
     'acquisition-update.json',
     'analysis.json',
+    'analysis-job.json',
     'avatars.json',
     'collection.json',
     'collection-update.json',

api/handlers/listhandler.py

@@ -610,62 +610,13 @@ class AnalysesHandler(ListHandler):
 
     def post(self, cont_name, list_name, **kwargs):
         """
-        .. http:post:: /api/(cont_name)/(cid)/analyses
-
-            Default behavior:
-                Creates an analysis object and uploads supplied input
-                and output files.
-            When param ``job`` is true:
-                Creates an analysis object and job object that reference
-                each other via ``job`` and ``destination`` fields. Job based
-                analyses are only allowed at the session level.
-
-            :param cont_name: one of ``projects``, ``sessions``, ``collections``
-            :type cont_name: string
-
-            :param cid: Container ID
-            :type cid: string
-
-            :query boolean job: a flag specifying the type of analysis
-
-            :statuscode 200: no error
-            :statuscode 400: Job-based analyses must be at the session level
-            :statuscode 400: Job-based analyses must have ``job`` and ``analysis`` maps in JSON body
-
-            **Example request**:
-
-            .. sourcecode:: http
-
-                POST /api/sessions/57081d06b386a6dc79ca383c/analyses HTTP/1.1
-
-                {
-                    "analysis": {
-                        "label": "Test Analysis 1"
-                    },
-                    "job" : {
-                        "gear": "dcm_convert",
-                        "inputs": {
-                            "dicom": {
-                                "type": "acquisition",
-                                "id": "57081d06b386a6dc79ca386b",
-                                "name" : "test_acquisition_dicom.zip"
-                            }
-                        },
-                        "tags": ["example"]
-                    }
-                }
-
-            **Example response**:
-
-            .. sourcecode:: http
-
-                HTTP/1.1 200 OK
-                Vary: Accept-Encoding
-                Content-Type: application/json; charset=utf-8
-                {
-                    "_id": "573cb66b135d87002660597c"
-                }
-
+        Default behavior:
+            Creates an analysis object and uploads supplied input
+            and output files.
+        When param ``job`` is true:
+            Creates an analysis object and job object that reference
+            each other via ``job`` and ``destination`` fields. Job based
+            analyses are only allowed at the session level.
         """
         _id = kwargs.pop('cid')
         permchecker, storage, _, payload_validator, _ = self._initialize_request(cont_name, list_name, _id)

api/handlers/reporthandler.py

@@ -58,7 +58,7 @@ def _get_result_list(output):
     throws APIReportException
     """
 
-    if output.get('ok', 0) is not 1.0:
+    if output.get('ok') == 1.0:
         result = output.get('result')
         if result is not None and len(result) > 0:
             return result

raml/api.raml

@@ -14,6 +14,25 @@ traits:
 resourceTypes:
   - container: !include resourceTypes/container.raml
   - container-item: !include resourceTypes/container-item.raml
+  - container-item-list-property: !include resourceTypes/container-item-list-property.raml
+  - container-item-list-property-append: !include resourceTypes/container-item-list-property-append.raml
+  - tags-list: !include resourceTypes/tags-list.raml
+  - tags-append: !include resourceTypes/tags-append.raml
+  - packfile-start: !include resourceTypes/packfile-start.raml
+  - packfile: !include resourceTypes/packfile.raml
+  - packfile-end: !include resourceTypes/packfile-end.raml
+  - file-list-upload: !include resourceTypes/file-list-upload.raml
+  - file-item: !include resourceTypes/file-item.raml
+  - permissions-list: !include resourceTypes/permissions-list.raml
+  - permissions-item: !include resourceTypes/permissions-item.raml
+  - notes-list: !include resourceTypes/notes-list.raml
+  - notes-item: !include resourceTypes/notes-item.raml
+  - analyses-list: !include resourceTypes/analyses-list.raml
+  - analysis-item: !include resourceTypes/analysis-item.raml
+  - analysis-files: !include resourceTypes/analysis-files.raml
+  - analysis-files-create-ticket-filename: !include resourceTypes/analysis-files-create-ticket-filename.raml
+  - analysis-notes-list: !include resourceTypes/analysis-notes-list.raml
+  - analysis-notes-item: !include resourceTypes/analysis-notes-item.raml
 
 /download: !include resources/download.raml
 /upload/label: !include resources/upload-by-label.raml
@@ -34,3 +53,4 @@ resourceTypes:
 /sessions: !include resources/sessions.raml
 /acquisitions: !include resources/acquisitions.raml
 /projects: !include resources/projects.raml
+/report: !include resources/report.raml

raml/examples/file_info_list.json

 [
   {
-    "name":"results.dcm.zip",
-    "modified":"2016-08-01T09:07:27.681792+00:00",
-    "size":7364859,
-    "mimetype":"application/octet-stream",
-    "hash":"v0-sha384-768412320f7b0aa5812fce428dc4706b3cae50e02a64caa16a782249bfe8efc4b7ef1ccb126255d196047dfedf17a0a9",
-    "origin":{
-      "name":"user1",
-      "uid":"579f5a4f8120be0c0828d777"
-    },
-    "type":"dicom",
-    "tags":[],
-    "metadata":{},
-    "instrument":"instrument1",
-    "measurements":[]
+      "origin": {
+          "type": "job",
+          "id": "58063f24e5dc5b001657a87f"
+      },
+      "mimetype": "application/octet-stream",
+      "hash": "v0-sha384-12188e00a26650b2baa3f0195337dcf504f4362bb2136eef0cdbefb57159356b1355a0402fca0ab5ab081f21c305e5c2",
+      "name": "cortical_surface_right_hemisphere.obj",
+      "tags": [],
+      "measurements": [],
+      "modified": "2016-10-18T15:26:35.701000+00:00",
+      "instrument": null,
+      "size": 21804112,
+      "type": "None",
+      "metadata": {}
+  }, {
+      "origin": {
+          "type": "job",
+          "id": "58065fa7e5dc5b001457a882"
+      },
+      "mimetype": "application/octet-stream",
+      "hash": "v0-sha384-12188e00a26650b2baa3f0195337dcf504f4362bb2136eef0cdbefb57159356b1355a0402fca0ab5ab081f21c305e5c2",
+      "name": "cortical_surface_right_hemisphere.obj",
+      "tags": [],
+      "measurements": [],
+      "modified": "2016-10-18T17:45:17.776000+00:00",
+      "instrument": null,
+      "metadata": {},
+      "type": "None",
+      "size": 21804112
   }
-]
\ No newline at end of file
+]

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/group-add-role.json

+{"access": "admin", "_id": "coltonlw@flywheel.io", "site":"local"}

raml/examples/input/group.json

 {
-  "name": "Test Group",
-  "_id": "test_group"
+  "name": "Example Group",
+  "_id": "example_group"
 }

raml/examples/input/note.json

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

raml/examples/input/permission-update.json

+{"access":"ro", "_id": "coltonlw@flywheel.io", "site":"local"}

raml/examples/input/permission.json

+{
+    "_id":"coltonlw@flywheel.io",
+    "site":"local",
+    "access":"admin"
+}

raml/examples/input/project-template.json

@@ -5,7 +5,7 @@
             "properties": {
                 "label": {
                     "type":     "string",
-                    "pattern":  "^(?i)test_pattern$" }
+                    "pattern":  "^test_pattern$" }
             }
         }
     },
@@ -30,7 +30,7 @@
                     "properties": {
                         "measurement": {
                             "type":     "string",
-                            "pattern":  "^(?i)functional$" }
+                            "pattern":  "^functional$" }
                     },
                     "required": ["measurement"]
                 },

raml/examples/input/tag.json

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

raml/examples/output/analysis-files-create-ticket.json

+{
+  "ticket": "57f2af23-a94c-426d-8521-11b2e8782020",
+  "filename": "exampledicom.zip",
+  "file_cnt": 1,
+  "size": 4525137
+}

raml/examples/output/analysis-item.json

+{
+    "files": [{
+        "origin": {
+            "type": "job",
+            "id": "58063f24e5dc5b001657a87f"
+        },
+        "mimetype": "application/octet-stream",
+        "hash": "v0-sha384-12188e00a26650b2baa3f0195337dcf504f4362bb2136eef0cdbefb57159356b1355a0402fca0ab5ab081f21c305e5c2",
+        "name": "cortical_surface_right_hemisphere.obj",
+        "tags": [],
+        "measurements": [],
+        "modified": "2016-10-18T15:26:35.701000+00:00",
+        "instrument": null,
+        "input": true,
+        "size": 21804112,
+        "type": "None",
+        "metadata": {}
+    }, {
+        "origin": {
+            "type": "job",
+            "id": "58065fa7e5dc5b001457a882"
+        },
+        "mimetype": "application/octet-stream",
+        "hash": "v0-sha384-12188e00a26650b2baa3f0195337dcf504f4362bb2136eef0cdbefb57159356b1355a0402fca0ab5ab081f21c305e5c2",
+        "name": "cortical_surface_right_hemisphere.obj",
+        "tags": [],
+        "measurements": [],
+        "modified": "2016-10-18T17:45:17.776000+00:00",
+        "instrument": null,
+        "output": true,
+        "metadata": {},
+        "type": "None",
+        "size": 21804112
+    }],
+    "created": "2016-10-18T17:45:11.778000+00:00",
+    "modified": "2016-10-18T17:45:11.778000+00:00",
+    "label": "cortex-demo 10/18/2016 13:45:5",
+    "job": {
+        "inputs": {
+            "anatomy": {
+                "type": "analysis",
+                "id": "58063f24e5dc5b001657a87e",
+                "name": "cortical_surface_right_hemisphere.obj"
+            }
+        },
+        "attempt": 1,
+        "name": "cortex-demo",
+        "tags": ["ad-hoc", "cortex-demo", "analysis"],
+        "destination": {
+            "type": "analysis",
+            "id": "58065fa7e5dc5b001457a881"
+        },
+        "request": {
+            "inputs": [{
+                "location": "/",
+                "type": "http",
+                "uri": "https://storage.googleapis.com/flywheel/gears/v1/scitran/cortex-demo/cortex-demo_manifest-labels_20160725T031837.331720Z.tar.gz",
+                "vu": "vu0:sha384:ssx5VWyFg7r8IBoOIphq7GaB_CymInQ1NxTV2WTDzglJLJ1-ktEbjLIHVABRzesV"
+            }, {
+                "type": "scitran",
+                "uri": "/jobs/58065fa7e5dc5b001457a882/config.json",
+                "location": "/flywheel/v0"
+            }, {
+                "type": "scitran",
+                "uri": "/sessions/58063e7ed213ed776045b320/analyses/58063f24e5dc5b001657a87e/files/cortical_surface_right_hemisphere.obj",
+                "location": "/flywheel/v0/input/anatomy"
+            }],
+            "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=analysis&id=58065fa7e5dc5b001457a881&job=58065fa7e5dc5b001457a882",
+                "location": "/flywheel/v0/output"
+            }]
+        },
+        "modified": "2016-10-18T17:45:21.344000+00:00",
+        "created": "2016-10-18T17:45:11.816000+00:00",
+        "state": "complete",
+        "config": {},
+        "id": "58065fa7e5dc5b001457a882"
+    },
+    "user": "canakgun@flywheel.io",
+    "_id": "58065fa7e5dc5b001457a881"
+}

raml/examples/output/file-download.json

+{"ticket": "1e975e3d-21e9-41f4-bb97-261f03d35ba1"}

raml/examples/output/note.json

+{
+    "_id":"580925ce9e512c57dc8a103b",
+    "text":"some text",
+    "created": "2016-10-21T17:19:40.899000+00:00",
+    "modified": "2016-10-21T17:19:40.899000+00:00",
+    "user": "coltonlw@flywheel.io"
+}

raml/examples/output/packfile-start.json

+{
+    "token":"57fe88cc9e512c5d2b5dcb0b"
+}

raml/examples/output/permission.json

+{"access": "admin", "_id": "coltonlw@flywheel.io", "site": "local"}

raml/examples/output/report-project.json

+{
+  "projects": [
+    {
+      "demographics_grid": {
+        "Black or African American": {
+          "Not Hispanic or Latino": {
+            "Male": 0,
+            "Unknown or Not Reported": 0,
+            "Female": 0
+          },
+          "Total": 0,
+          "Unknown or Not Reported": {
+            "Male": 0,
+            "Unknown or Not Reported": 0,
+            "Female": 0
+          },
+          "Hispanic or Latino": {
+            "Male": 0,
+            "Unknown or Not Reported": 0,
+            "Female": 0
+          }
+        },
+        "Unknown or Not Reported": {
+          "Not Hispanic or Latino": {
+            "Male": 0,
+            "Unknown or Not Reported": 0,
+            "Female": 0
+          },
+          "Total": 1,
+          "Unknown or Not Reported": {
+            "Male": 1,
+            "Unknown or Not Reported": 0,
+            "Female": 0
+          },
+          "Hispanic or Latino": {
+            "Male": 0,
+            "Unknown or Not Reported": 0,
+            "Female": 0
+          }
+        },
+        "American Indian or Alaska Native": {
+          "Not Hispanic or Latino": {
+            "Male": 0,
+            "Unknown or Not Reported": 0,
+            "Female": 0
+          },
+          "Total": 0,
+          "Unknown or Not Reported": {
+            "Male": 0,
+            "Unknown or Not Reported": 0,
+            "Female": 0
+          },
+          "Hispanic or Latino": {
+            "Male": 0,
+            "Unknown or Not Reported": 0,
+            "Female": 0
+          }
+        },
+        "Asian": {
+          "Not Hispanic or Latino": {
+            "Male": 0,
+            "Unknown or Not Reported": 0,
+            "Female": 0
+          },
+          "Total": 0,
+          "Unknown or Not Reported": {
+            "Male": 0,
+            "Unknown or Not Reported": 0,
+            "Female": 0
+          },
+          "Hispanic or Latino": {
+            "Male": 0,
+            "Unknown or Not Reported": 0,
+            "Female": 0
+          }
+        },
+        "White": {
+          "Not Hispanic or Latino": {
+            "Male": 0,
+            "Unknown or Not Reported": 0,
+            "Female": 0
+          },
+          "Total": 0,
+          "Unknown or Not Reported": {
+            "Male": 0,
+            "Unknown or Not Reported": 0,
+            "Female": 0
+          },
+          "Hispanic or Latino": {
+            "Male": 0,
+            "Unknown or Not Reported": 0,
+            "Female": 0
+          }
+        },
+        "Total": {
+          "Not Hispanic or Latino": {
+            "Male": 0,
+            "Unknown or Not Reported": 0,
+            "Female": 0
+          },
+          "Total": 0,
+          "Unknown or Not Reported": {
+            "Male": 1,
+            "Unknown or Not Reported": 0,
+            "Female": 0
+          },
+          "Hispanic or Latino": {
+            "Male": 0,
+            "Unknown or Not Reported": 0,
+            "Female": 0
+          }
+        },
+        "Native Hawaiian or Other Pacific Islander": {
+          "Not Hispanic or Latino": {
+            "Male": 0,
+            "Unknown or Not Reported": 0,
+            "Female": 0
+          },
+          "Total": 0,
+          "Unknown or Not Reported": {
+            "Male": 0,
+            "Unknown or Not Reported": 0,
+            "Female": 0
+          },
+          "Hispanic or Latino": {
+            "Male": 0,
+            "Unknown or Not Reported": 0,
+            "Female": 0
+          }
+        },
+        "More Than One Race": {
+          "Not Hispanic or Latino": {
+            "Male": 0,
+            "Unknown or Not Reported": 0,
+            "Female": 0
+          },
+          "Total": 0,
+          "Unknown or Not Reported": {
+            "Male": 0,
+            "Unknown or Not Reported": 0,
+            "Female": 0
+          },
+          "Hispanic or Latino": {
+            "Male": 0,
+            "Unknown or Not Reported": 0,
+            "Female": 0
+          }
+        }
+      },
+      "male_count": 1,
+      "group_name": "test-group",
+      "over_18_count": 1,
+      "under_18_count": 0,
+      "female_count": 0,
+      "subjects_count": 1,
+      "other_count": 0,
+      "name": "test-project-1",
+      "session_count": 1,
+      "admins": [
+        "Colton LW"
+      ],
+      "demographics_total": 1
+    }
+  ]
+}