[SYNPY-1634, SYNPY-1377] Use new OOP models in tutorials (#1241)

* Update several tutorials to use OOP model

Author: thomasyu888

README.md

@@ -3,12 +3,12 @@ Python Synapse Client
 
 Branch  | Build Status
 --------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
-develop | [![Build Status develop branch](https://github.com/Sage-Bionetworks/synapsePythonClient/workflows/build/badge.svg?branch=develop)](https://github.com/Sage-Bionetworks/synapsePythonClient/actions?query=branch%3Adevelop)
-master  | [![Build Status master branch](https://github.com/Sage-Bionetworks/synapsePythonClient/workflows/build/badge.svg?branch=master)](https://github.com/Sage-Bionetworks/synapsePythonClient/actions?query=branch%3Amaster)
+develop | [![Build Status develop branch](https://github.com/Sage-Bionetworks/synapsePythonClient/actions/workflows/build.yml/badge.svg?branch=develop)](https://github.com/Sage-Bionetworks/synapsePythonClient/actions?query=branch%3Adevelop)
+master  | [![Build Status master branch](https://github.com/Sage-Bionetworks/synapsePythonClient/actions/workflows/build.yml/badge.svg?branch=master)](https://github.com/Sage-Bionetworks/synapsePythonClient/actions?query=branch%3Amaster)
 
 [![Get the synapseclient from PyPI](https://img.shields.io/pypi/v/synapseclient.svg)](https://pypi.python.org/pypi/synapseclient/) [![Supported Python Versions](https://img.shields.io/pypi/pyversions/synapseclient.svg)](https://pypi.python.org/pypi/synapseclient/)
 
-A Python client for [Sage Bionetworks'](https://www.sagebase.org) [Synapse](https://www.synapse.org/), a collaborative, open-source research platform that allows teams to share data, track analyses, and collaborate. The Python client can be used as a library for development of software that communicates with Synapse or as a command-line utility.
+A Python client for [Sage Bionetworks'](https://sagebionetworks.org/) [Synapse](https://www.synapse.org/), a collaborative, open-source research platform that allows teams to share data, track analyses, and collaborate. The Python client can be used as a library for development of software that communicates with Synapse or as a command-line utility.
 
 There is also a [Synapse client for R](https://github.com/Sage-Bionetworks/synapser/).
 
@@ -156,15 +156,15 @@ synapseutils.syncToSynapse(
 #### Store a Project to Synapse
 ```
 import synapseclient
-from synapseclient.entity import Project
+from synapseclient.models import Project
 
 syn = synapseclient.Synapse()
 
 ## log in using auth token
 syn.login(authToken='auth_token')
 
 project = Project('My uniquely named project')
-project = syn.store(project)
+project.store()
 
 print(project.id)
 print(project)
@@ -173,14 +173,15 @@ print(project)
 #### Store a Folder to Synapse (Does not upload files within the folder)
 ```
 import synapseclient
+from synapseclient.models import Folder
 
 syn = synapseclient.Synapse()
 
 ## log in using auth token
 syn.login(authToken='auth_token')
 
-folder = Folder(name='my_folder', parent="syn123")
-folder = syn.store(folder)
+folder = Folder(name='my_folder', parent_id="syn123")
+folder.store()
 
 print(folder.id)
 print(folder)
@@ -190,17 +191,18 @@ print(folder)
 #### Store a File to Synapse
 ```
 import synapseclient
+from synapseclient.models import File
 
 syn = synapseclient.Synapse()
 
 ## log in using auth token
 syn.login(authToken='auth_token')
 
 file = File(
-    path=filepath,
-    parent="syn123",
+    path="path/to/file.txt",
+    parent_id="syn123",
 )
-file = syn.store(file)
+file.store()
 
 print(file.id)
 print(file)
@@ -209,14 +211,15 @@ print(file)
 #### Get a data matrix
 ```
 import synapseclient
+from synapseclient.models import File
 
 syn = synapseclient.Synapse()
 
 ## log in using auth token
 syn.login(authToken='auth_token')
 
 ## retrieve a 100 by 4 matrix
-matrix = syn.get('syn1901033')
+matrix = File(id='syn1901033').get()
 
 ## inspect its properties
 print(matrix.name)

docs/guides/data_storage.md

@@ -24,12 +24,13 @@ If you are changing the storage location of an existing folder to a user specifi
 2. Create a folder and configure it to use external S3 storage:
 
 ```python
+from synapseclient.models import Folder
 # create a new folder to use with external S3 storage
-folder = syn.store(Folder(name=folder_name, parent=parent))
+folder = Folder(name=folder_name, parent_id=parent).store()
 # You may also use an existing folder like:
 # folder = syn.get("syn123")
 folder, storage_location, project_setting = syn.create_s3_storage_location(
-    folder=folder,
+    folder=folder.id,
     bucket_name='my-external-synapse-bucket',
     base_key='path/within/bucket',
  )
@@ -48,11 +49,12 @@ If you are changing the storage location of an existing project to a user specif
 2. Create a project and configure it to use external S3 storage:
 
 ```python
+from synapseclient.models import Project
 # create a new, or retrieve an existing project to use with external S3 storage
-project = syn.store(Project(name="my_project_name"))
+project = Project(name="my_project_name").store()
 project_storage, storage_location, project_setting = syn.create_s3_storage_location(
     # Despite the KW argument name, this can be a project or folder
-    folder=project,
+    folder=project.id,
     bucket_name='my-external-synapse-bucket',
     base_key='path/within/bucket',
 )
@@ -64,6 +66,8 @@ storage_location_id = storage_location['storageLocationId']
 Once an external S3 storage folder exists, you can interact with it as you would any other folder using Synapse tools. If you wish to add an object that is stored within the bucket to Synapse you can do that by adding a file handle for that object using the Python client and then storing the file to that handle.
 
 ```python
+from synapseclient.models import File
+
 parent_synapse_folder_id = 'syn123'
 local_file_path = '/path/to/local/file'
 bucket = 'my-external-synapse-bucket'
@@ -84,8 +88,8 @@ file_handle = syn.create_external_s3_file_handle(
     local_file_path,
     parent=parent_synapse_folder_id,
 )
-file = File(parentId=folder['id'], dataFileHandleId=file_handle['id'])
-file_entity = syn.store(file)
+file_entity = File(parent_id=folder['id'], data_file_handle_id=file_handle['id'])
+file_entity.store()
 ```
 
 ## Storage location migration

docs/guides/validate_annotations.md

@@ -2,14 +2,13 @@
 
 [![Supported Python Versions](https://img.shields.io/pypi/pyversions/synapseclient.svg)](https://pypi.org/project/synapseclient/)
 
-### **Notice for the upcoming v5.0 release:**
-
-- The upcoming v5.0 release will include a number of breaking changes. Take a look at
-this [pubpub](https://sagebionetworks.pubpub.org/pub/828a3x4k/release/1) article
-detailing some of the changes.
-- A release date has not been set. A number of these changes will be available within
-the 4.x.x versions hidden behind optional feature flags or different import paths. Any
-breaking changes will not be included until v5.0.
+!!! note "Notice for the upcoming v5.0 release"
+    - The upcoming v5.0 release will include a number of breaking changes. Take a look at
+    this [pubpub](https://sagebionetworks.pubpub.org/pub/828a3x4k/release/1) article
+    detailing some of the changes.
+    - A release date has not been set. A number of these changes will be available within
+    the 4.x.x versions hidden behind optional feature flags or different import paths. Any
+    breaking changes will not be included until v5.0.
 
 The `synapseclient` package provides an interface to [Synapse](http://www.synapse.org), a collaborative, open-source research platform that allows teams to share data, track analyses, and collaborate, providing support for: