Merge branch 'master' of https://github.com/superannotateai/superannotate-python-sdk

Author: agyurjin

.gitignore

@@ -133,3 +133,6 @@ sample_tif_files
 
 # Vscode settings folder
 .vscode/
+
+# python virtual env for SDK testing
+venv_sa_conv

docs/source/cli.rst

@@ -36,6 +36,19 @@ To initialize CLI (and SDK) with team token:
 
 ----------
 
+.. _ref_create_project:
+
+Creating a project
+~~~~~~~~~~~~~~~~~~
+
+To create a new project:
+
+.. code-block:: bash
+
+   superannotate create-project --name <project_name> --description <project_description> --type <project_type Vector or Pixel>
+
+----------
+
 .. _ref_upload_images:
 
 Uploading images

docs/source/superannotate.sdk.rst

@@ -110,6 +110,7 @@ _________________
 
 .. autofunction:: superannotate.get_team_metadata
 .. autofunction:: superannotate.invite_contributor_to_team
+.. autofunction:: superannotate.delete_contributor_to_team_invitation
 
 ----------
 

superannotate/__init__.py

@@ -61,7 +61,10 @@
     upload_preannotations_from_folder_to_project, upload_video_to_project,
     upload_videos_from_folder_to_project
 )
-from .db.teams import get_team_metadata, invite_contributor_to_team
+from .db.teams import (
+    delete_contributor_to_team_invitation, get_team_metadata,
+    invite_contributor_to_team
+)
 from .db.users import search_team_contributors
 from .dicom_converter import dicom_to_rgb_sequence
 from .exceptions import (

superannotate/__main__.py

@@ -44,7 +44,9 @@ def main():
     command = sys.argv[1]
     further_args = sys.argv[2:]
 
-    if command == "upload-images":
+    if command == "create-project":
+        create_project(further_args)
+    elif command == "upload-images":
         image_upload(further_args)
     elif command == "upload-videos":
         video_upload(further_args)
@@ -122,7 +124,8 @@ def preannotations_upload(args, annotations=False):
         )
         args.folder = tempdir_path
     sa.create_annotation_classes_from_classes_json(
-        args.project, Path(args.folder) / "classes" / "classes.json"
+        args.project,
+        Path(args.folder) / "classes" / "classes.json"
     )
 
     if annotations:
@@ -135,6 +138,20 @@ def preannotations_upload(args, annotations=False):
         )
 
 
+def create_project(args):
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--name', required=True, help='Project name to create')
+    parser.add_argument(
+        '--description', required=True, help='Project description'
+    )
+    parser.add_argument(
+        '--type', required=True, help='Project type Vector or Pixel'
+    )
+    args = parser.parse_args(args)
+
+    sa.create_project(args.name, args.description, args.type)
+
+
 def video_upload(args):
     parser = argparse.ArgumentParser()
     parser.add_argument(

superannotate/analytics/common.py

@@ -183,10 +183,17 @@ def aggregate_annotations_as_df(
         )
     classes_json = json.load(open(classes_path))
     class_name_to_color = {}
+    class_group_name_to_values = {}
     for annotation_class in classes_json:
         name = annotation_class["name"]
         color = annotation_class["color"]
         class_name_to_color[name] = color
+        class_group_name_to_values[name] = {}
+        for attribute_group in annotation_class["attribute_groups"]:
+            class_group_name_to_values[name][attribute_group["name"]] = []
+            for attribute in attribute_group["attributes"]:
+                class_group_name_to_values[name][attribute_group["name"]
+                                                ].append(attribute["name"])
 
     def __append_annotation(annotation_dict):
         for annotation_key in annotation_data:
@@ -258,10 +265,12 @@ def __get_image_metadata(image_name, annotations):
                 continue
             annotation_instance_id += 1
             annotation_class_name = annotation.get("className")
-            if annotation_class_name is None:
-                raise SABaseException(
-                    0, "Annotation class not found in classes.json"
+            if annotation_class_name is None or annotation_class_name not in class_name_to_color:
+                logger.warning(
+                    "Annotation class %s not found in classes json. Skipping.",
+                    annotation_class_name
                 )
+                continue
             annotation_class_color = class_name_to_color[annotation_class_name]
             annotation_group_id = annotation.get("groupId")
             annotation_locked = annotation.get("locked")
@@ -332,37 +341,50 @@ def __get_image_metadata(image_name, annotations):
                 }
                 annotation_dict.update(image_metadata)
                 __append_annotation(annotation_dict)
-
-            for attribute in attributes:
-
-                attribute_group = attribute.get("groupName")
-                attribute_name = attribute.get('name')
-                annotation_dict = {
-                    "imageName": image_name,
-                    "instanceId": annotation_instance_id,
-                    "className": annotation_class_name,
-                    "attributeGroupName": attribute_group,
-                    "attributeName": attribute_name,
-                    "type": annotation_type,
-                    "locked": annotation_locked,
-                    "visible": annotation_visible,
-                    "trackingId": annotation_tracking_id,
-                    "meta": annotation_meta,
-                    "error": annotation_error,
-                    "probability": annotation_probability,
-                    "pointLabels": annotation_point_labels,
-                    "classColor": annotation_class_color,
-                    "groupId": annotation_group_id,
-                    "createdAt": annotation_created_at,
-                    "creatorRole": annotation_creator_role,
-                    "creatorEmail": annotation_creator_email,
-                    "creationType": annotation_creation_type,
-                    "updatedAt": annotation_updated_at,
-                    "updatorRole": annotation_updator_role,
-                    "updatorEmail": annotation_updator_email
-                }
-                annotation_dict.update(image_metadata)
-                __append_annotation(annotation_dict)
+            else:
+                for attribute in attributes:
+                    attribute_group = attribute.get("groupName")
+                    attribute_name = attribute.get('name')
+                    if attribute_group not in class_group_name_to_values[
+                        annotation_class_name]:
+                        logger.warning(
+                            "Annotation class group %s not in classes json. Skipping.",
+                            attribute_group
+                        )
+                        continue
+                    if attribute_name not in class_group_name_to_values[
+                        annotation_class_name][attribute_group]:
+                        logger.warning(
+                            "Annotation class group value %s not in classes json. Skipping.",
+                            attribute_name
+                        )
+                        continue
+                    annotation_dict = {
+                        "imageName": image_name,
+                        "instanceId": annotation_instance_id,
+                        "className": annotation_class_name,
+                        "attributeGroupName": attribute_group,
+                        "attributeName": attribute_name,
+                        "type": annotation_type,
+                        "locked": annotation_locked,
+                        "visible": annotation_visible,
+                        "trackingId": annotation_tracking_id,
+                        "meta": annotation_meta,
+                        "error": annotation_error,
+                        "probability": annotation_probability,
+                        "pointLabels": annotation_point_labels,
+                        "classColor": annotation_class_color,
+                        "groupId": annotation_group_id,
+                        "createdAt": annotation_created_at,
+                        "creatorRole": annotation_creator_role,
+                        "creatorEmail": annotation_creator_email,
+                        "creationType": annotation_creation_type,
+                        "updatedAt": annotation_updated_at,
+                        "updatorRole": annotation_updator_role,
+                        "updatorEmail": annotation_updator_email
+                    }
+                    annotation_dict.update(image_metadata)
+                    __append_annotation(annotation_dict)
 
     df = pd.DataFrame(annotation_data)
 

superannotate/db/annotation_classes.py

@@ -160,19 +160,40 @@ def create_annotation_classes_from_classes_json(
         else:
             new_classes.append(cs)
 
-    params = {
-        'team_id': team_id,
-        'project_id': project_id,
-    }
-    data = {"classes": new_classes}
-    response = _api.send_request(
-        req_type='POST', path='/classes', params=params, json_req=data
-    )
-    if not response.ok:
-        raise SABaseException(
-            response.status_code, "Couldn't create classes " + response.text
+    res = []
+
+    def del_unn(d):
+        for s in [
+            "updatedAt", "createdAt", "id", "project_id", "group_id",
+            "class_id", "count"
+        ]:
+            if s in d:
+                del d[s]
+
+    for annotation_class in new_classes:
+        del_unn(annotation_class)
+        for attribute_group in annotation_class["attribute_groups"]:
+            del_unn(attribute_group)
+            for attribute in attribute_group["attributes"]:
+                del_unn(attribute)
+
+    CHUNK_SIZE = 2000
+    for i in range(0, len(new_classes), CHUNK_SIZE):
+        params = {
+            'team_id': team_id,
+            'project_id': project_id,
+        }
+        data = {"classes": new_classes[i:i + CHUNK_SIZE]}
+        response = _api.send_request(
+            req_type='POST', path='/classes', params=params, json_req=data
         )
-    res = response.json()
+        if not response.ok:
+            raise SABaseException(
+                response.status_code, "Couldn't create classes " + response.text
+            )
+        res += response.json()
+
+    assert len(res) == len(new_classes)
     return res
 
 
@@ -280,12 +301,13 @@ def fill_class_and_attribute_names(annotations_json, annotation_classes_dict):
             r["className"] = annotation_classes_dict[r["classId"]]["name"]
             if "attributes" in r:
                 for attribute in r["attributes"]:
-                    attribute["groupName"] = annotation_classes_dict[
-                        r["classId"]]["attribute_groups"][attribute["groupId"]
-                                                         ]["name"]
-                    attribute["name"] = annotation_classes_dict[
-                        r["classId"]]["attribute_groups"][
-                            attribute["groupId"]]["attributes"][attribute["id"]]
+                    if "groupId" in attribute and "id" in "attribute":
+                        attribute["groupName"] = annotation_classes_dict[
+                            r["classId"]]["attribute_groups"][
+                                attribute["groupId"]]["name"]
+                        attribute["name"] = annotation_classes_dict[
+                            r["classId"]]["attribute_groups"][attribute[
+                                "groupId"]]["attributes"][attribute["id"]]
 
 
 def fill_class_and_attribute_ids(annotation_json, annotation_classes_dict):
@@ -299,15 +321,32 @@ def fill_class_and_attribute_ids(annotation_json, annotation_classes_dict):
             logger.warning(
                 "Couldn't find annotation class %s", annotation_class_name
             )
+            continue
         class_id = annotation_classes_dict[annotation_class_name]["id"]
         ann["classId"] = class_id
         for attribute in ann["attributes"]:
-            attribute["groupId"] = annotation_classes_dict[
+            if attribute["groupName"] in annotation_classes_dict[
+                annotation_class_name]["attribute_groups"]:
+                attribute["groupId"] = annotation_classes_dict[
+                    annotation_class_name]["attribute_groups"][
+                        attribute["groupName"]]["id"]
+            else:
+                logger.warning(
+                    "Couldn't find annotation group %s", attribute["groupName"]
+                )
+                continue
+            if attribute["name"] in annotation_classes_dict[
                 annotation_class_name]["attribute_groups"][
-                    attribute["groupName"]]["id"]
-            attribute["id"] = annotation_classes_dict[annotation_class_name][
-                "attribute_groups"][attribute["groupName"]]["attributes"][
-                    attribute["name"]]
+                    attribute["groupName"]]["attributes"]:
+                attribute["id"] = annotation_classes_dict[
+                    annotation_class_name]["attribute_groups"][
+                        attribute["groupName"]]["attributes"][attribute["name"]]
+            else:
+                logger.warning(
+                    "Couldn't find annotation name %s in annotation group %s",
+                    attribute["name"], attribute["groupName"]
+                )
+                del attribute["groupId"]
 
 
 def get_annotation_classes_id_to_name(annotation_classes):

superannotate/db/teams.py

@@ -52,18 +52,25 @@ def get_team_metadata(convert_users_role_to_string=False):
     return res
 
 
-# def delete_team_contributor_invitation(invitation):
-#     """Deletes team contributor invitation
-
-#     :param invite: invitation metadata returned from invite_contributor_to_team
-#     :type project: dict
-#     """
-#     data = {'token': invitation["token"], 'e_mail': invitation['email']}
-#     response = _api.send_request(
-#         req_type='DELETE', path=f'/team/{_api.team_id}/invite', json_req=data
-#     )
-#     if not response.ok:
-#         raise SABaseException(
-#             response.status_code,
-#             "Couldn't delete contributor invite. " + response.text
-#         )
+def delete_contributor_to_team_invitation(email):
+    """Deletes team contributor invitation
+
+    :param email: invitation email
+    :type email: str
+    """
+    team_metadata = get_team_metadata()
+    for invite in team_metadata["pending_invitations"]:
+        if invite["email"] == email:
+            break
+    else:
+        raise SABaseException(0, "Couldn't find user " + email + " invitation")
+
+    data = {'token': invite["token"], 'e_mail': invite['email']}  # pylint: disable=undefined-loop-variable
+    response = _api.send_request(
+        req_type='DELETE', path=f'/team/{_api.team_id}/invite', json_req=data
+    )
+    if not response.ok:
+        raise SABaseException(
+            response.status_code,
+            "Couldn't delete contributor invite. " + response.text
+        )

superannotate/db/users.py

@@ -62,6 +62,8 @@ def get_team_contributor_metadata(email):
         if user["email"] == email:
             results.append(user)
 
-    if len(results) > 1 or len(results) == 0:
+    if len(results) == 0:
+        raise SABaseException(0, "No user with email " + email + " found.")
+    if len(results) > 1:
         raise SABaseException(0, "Email " + email + " malformed.")
     return results[0]

superannotate/version.py

@@ -1 +1 @@
-__version__ = "2.3.5"
+__version__ = "2.3.9"