POST process_json endpoint (#181)

* adding new rest endpoint for posting JSON

* adds recursive Dataset endpoint

* linting

* lockfile update

* version increment

client/package.json

@@ -1,6 +1,6 @@
 {
   "name": "dive-dsa",
-  "version": "1.10.17",
+  "version": "1.10.18",
   "author": {
     "name": "Kitware, Inc.",
     "email": "Bryon.Lewis@kitware.com"
@@ -25,7 +25,7 @@
   "main": "lib/index.js",
   "types": "lib/types/index.d.ts",
   "dependencies": {
-    "vue-girder-slicer-cli-ui": "0.0.8",
+    "vue-girder-slicer-cli-ui": "0.0.9",
     "@flatten-js/interval-tree": "^1.0.11",
     "@girder/components": "^3.2.0",
     "@mdi/font": "^6.2.95",

client/yarn.lock

@@ -11019,10 +11019,10 @@ vue-eslint-parser@^9.0.1, vue-eslint-parser@^9.0.3, vue-eslint-parser@^9.3.1, vu
     lodash "^4.17.21"
     semver "^7.3.6"
 
-vue-girder-slicer-cli-ui@0.0.8:
-  version "0.0.8"
-  resolved "https://registry.yarnpkg.com/vue-girder-slicer-cli-ui/-/vue-girder-slicer-cli-ui-0.0.8.tgz#7c6d91598f54f469e6306cf2fdf9a503b8284099"
-  integrity sha512-xCVkzDmOTKfukFyYw4NawfOLAelF6iTdyJXDbxQZ6xpdDhuGsJdzlE2xDxQZcGdV0vLX13wWNZvIA+Wn7CMhAQ==
+vue-girder-slicer-cli-ui@0.0.9:
+  version "0.0.9"
+  resolved "https://registry.yarnpkg.com/vue-girder-slicer-cli-ui/-/vue-girder-slicer-cli-ui-0.0.9.tgz#7725fbfb8f6b92f917b1e1fc264ad0e868ae47b1"
+  integrity sha512-IYaecdkcAHgnCvRBaDxLxUrAmYr5Ft70NPwUGLmYvlP95HHgTObuIEqke4b2WU4AIFabwhlP9LeU5KGaUEJW5A==
   dependencies:
     "@jamescoyle/vue-icon" "^0.1.2"
     "@mdi/js" "^7.2.96"

server/dive_server/crud_dataset.py

@@ -179,6 +179,19 @@ def get_task_defaults(
     )
 
 
+def get_recursive_datasets(
+    dsFolder: types.GirderModel, user: types.GirderUserModel, datasetList: List[types.GirderModel], limit: int = -1
+):
+    subFolders = list(Folder().childFolders(dsFolder, 'folder', user))
+    for child in subFolders:
+        if child.get('meta', {}).get(constants.DatasetMarker, False):
+            if limit == -1 or len(datasetList) < limit:
+                datasetList.append(child)
+            else:
+                return
+        get_recursive_datasets(child, user, datasetList, limit)
+
+
 def get_media(
     dsFolder: types.GirderModel, user: types.GirderUserModel
 ) -> models.DatasetSourceMedia:

server/dive_server/views_annotation.py

@@ -10,6 +10,7 @@
 from girder.models.folder import Folder
 
 from dive_utils import constants, models, setContentDisposition
+from dive_utils.serializers import dive, viame
 
 from . import crud, crud_annotation
 
@@ -44,6 +45,7 @@ def __init__(self, resourceName):
         self.route("PATCH", (), self.save_annotations)
         self.route("PUT", ("track",), self.update_tracks)
         self.route("POST", ("rollback",), self.rollback)
+        self.route("POST", ("process_json",), self.process_json)
 
     @access.user
     @autoDescribeRoute(GetAnnotationParams)
@@ -195,6 +197,59 @@ def rollback(self, folder, revision):
         crud.verify_dataset(folder)
         crud_annotation.rollback(folder, revision)
 
+    @access.user
+    @autoDescribeRoute(
+        Description("Upload a Complete TrackJSON File to system and process it for attributes")
+        .modelParam("folderId", **DatasetModelParam, level=AccessType.WRITE)
+        .jsonParam(
+            "body",
+            "TrackJSON data to upload to the folderId",
+            paramType="body",
+            requireObject=True,
+        )
+        .param(
+            "additive",
+            "Whether to add new annotations to existing ones.  Annotations \
+            will be added with Ids starting at the last existing Id+1",
+            paramType="query",
+            dataType="boolean",
+            default=False,
+            required=False,
+        )
+        .param(
+            "additivePrepend",
+            "When using additive the prepend to types: I.E. 'prepend_type' \
+            so the string will be added to all types that are imported",
+            paramType="query",
+            dataType="string",
+            default='',
+            required=False,
+        )
+    )
+    def process_json(self, folder, body, additive, additivePrepend):
+        crud.verify_dataset(folder)
+        user = self.getCurrentUser()
+        annotations = dive.migrate(body)
+        _oldannotations, attributes = viame.load_json_as_track_and_attributes(body)
+        if annotations:
+            updated_tracks = annotations['tracks'].values()
+            if additive:  # get annotations and add them to the end
+                tracks = crud_annotation.add_annotations(
+                    folder, annotations['tracks'], additivePrepend
+                )
+                updated_tracks = tracks.values()
+            print(f'Saving Annotations: {user}')
+            crud_annotation.save_annotations(
+                folder,
+                user,
+                upsert_tracks=updated_tracks,
+                upsert_groups=annotations['groups'].values(),
+                overwrite=True,
+                description=f'POST trackJSON from {user["login"]}',
+            )
+        if attributes:
+            crud.saveImportAttributes(folder, attributes, user)
+
     @access.user
     @autoDescribeRoute(
         Description("Get all labels visible to a particular user")

server/dive_server/views_dataset.py

@@ -56,6 +56,7 @@ def __init__(self, resourceName):
         self.route("GET", (":id",), self.get_meta)
         self.route("GET", (":id", "media"), self.get_media)
         self.route("GET", (":id", "task-defaults"), self.get_task_defaults)
+        self.route("GET", (":id", "recursive"), self.get_recursive)
         self.route("GET", ("export",), self.export)
         self.route("GET", (":id", "configuration"), self.get_configuration)
         self.route("GET", (":id", "export_configuration"), self.export_configuration)
@@ -509,6 +510,27 @@ def get_media(self, folder):
     def get_task_defaults(self, folder):
         return crud_dataset.get_task_defaults(folder, self.getCurrentUser()).dict(exclude_none=True)
 
+    @access.public(scope=TokenScope.DATA_READ, cookie=True)
+    @autoDescribeRoute(
+        Description("Get a Recursive list of all DIVE Datasets within a parent folder").modelParam(
+            "id",
+            level=AccessType.READ,
+            **DatasetModelParam,
+        )
+        .param(
+            "limit",
+            "Limit the number of Datasets returned, -1 is no limit",
+            dataType="integer",
+            default=-1,
+            required=False,
+        )
+
+    )
+    def get_recursive(self, folder, limit):
+        datasetList = []
+        crud_dataset.get_recursive_datasets(folder, self.getCurrentUser(), datasetList, limit)
+        return datasetList
+
     @access.public(scope=TokenScope.DATA_READ, cookie=True)
     @autoDescribeRoute(
         Description("Export all selected datasets")