Object-Orientated Models
Contained within this file are experimental interfaces for working with the Synapse Python Client. Unless otherwise noted these interfaces are subject to change at any time. Use at your own risk.
Sample Scripts:¶
Working with a project
"""
Expects that ~/temp exists and is a directory.
The purpose of this script is to demonstrate how to use the new OOP interface for projects.
The following actions are shown in this script:
1. Creating a project
2. Retrieving a project by id or name
3. Upserting data on a project
4. Storing several files to a project
5. Storing several folders in a project
6. Updating the annotations in bulk for a number of folders and files
7. Downloading an entire project structure to disk
8. Copy a project and all content to a new project
9. Deleting a project
"""
import os
import uuid
from datetime import date, datetime, timedelta, timezone
import synapseclient
from synapseclient.models import File, Folder, Project
syn = synapseclient.Synapse(debug=True)
syn.login()
def create_random_file(
path: str,
) -> None:
"""Create a random file with random data."""
with open(path, "wb") as f:
f.write(os.urandom(1))
def store_project():
# Creating annotations for my project ==================================================
my_annotations = {
"my_single_key_string": "a",
"my_key_string": ["b", "a", "c"],
"my_key_bool": [False, False, False],
"my_key_double": [1.2, 3.4, 5.6],
"my_key_long": [1, 2, 3],
"my_key_date": [date.today(), date.today() - timedelta(days=1)],
"my_key_datetime": [
datetime.today(),
datetime.today() - timedelta(days=1),
datetime.now(tz=timezone(timedelta(hours=-5))),
datetime(2023, 12, 7, 13, 0, 0, tzinfo=timezone(timedelta(hours=0))),
datetime(2023, 12, 7, 13, 0, 0, tzinfo=timezone(timedelta(hours=-7))),
],
"annotation_i_want_to_delete": "I want to delete this annotation",
}
# 1) Creating a project ==============================================================
project = Project(
name="my_new_project_for_testing",
annotations=my_annotations,
description="This is a project with random data.",
alias="my_project_alias_" + str(uuid.uuid4()).replace("-", "_"),
)
project = project.store()
print(f"Project created with id: {project.id}")
# 2) Retrieving a project by id or name ==============================================
project = Project(name="my_new_project_for_testing").get()
print(f"Project retrieved by name: {project.name} with id: {project.id}")
project = Project(id=project.id).get()
print(f"Project retrieved by id: {project.name} with id: {project.id}")
# 3) Upserting data on a project =====================================================
# When you have not already use `.store()` or `.get()` on a project any updates will
# be a non-destructive upsert. This means that if the project does not exist it will
# be created, if it does exist it will be updated.
project = Project(
name="my_new_project_for_testing", description="my new description"
).store()
print(f"Project description updated to {project.description}")
# After the instance has interacted with Synapse any changes will be destructive,
# meaning changes in the data will act as a replacement instead of an addition.
print(f"Annotations before update: {project.annotations}")
del project.annotations["annotation_i_want_to_delete"]
project = project.store()
print(f"Annotations after update: {project.annotations}")
# 4) Storing several files to a project ==============================================
files_to_store = []
for loop in range(1, 10):
name_of_file = f"my_file_with_random_data_{loop}.txt"
path_to_file = os.path.join(os.path.expanduser("~/temp"), name_of_file)
create_random_file(path_to_file)
file = File(
path=path_to_file,
name=name_of_file,
annotations=my_annotations,
)
files_to_store.append(file)
project.files = files_to_store
project = project.store()
# 5) Storing several folders in a project ============================================
folders_to_store = []
for loop in range(1, 10):
folder_to_store = Folder(
name=f"my_folder_for_this_project_{loop}",
annotations=my_annotations,
)
folders_to_store.append(folder_to_store)
project.folders = folders_to_store
print(
f"Storing project ({project.id}) with {len(project.folders)} folders and {len(project.files)} files"
)
project = project.store()
# 6) Updating the annotations in bulk for a number of folders and files ==============
project_copy = Project(id=project.id).sync_from_synapse(download_file=False)
print(
f"Found {len(project_copy.files)} files and {len(project_copy.folders)} folder at the root level for {project_copy.name} with id: {project_copy.id}"
)
new_annotations = {
"my_new_key_string": ["b", "a", "c"],
}
for file in project_copy.files:
file.annotations = new_annotations
for folder in project_copy.folders:
folder.annotations = new_annotations
project_copy.store()
# 7) Downloading an entire project structure to disk =================================
print(f"Downloading project ({project.id}) to ~/temp")
Project(id=project.id).sync_from_synapse(
download_file=True, path="~/temp/recursiveDownload", recursive=True
)
# 8) Copy a project and all content to a new project =================================
project_to_delete = Project(
name="my_new_project_I_want_to_delete_" + str(uuid.uuid4()).replace("-", "_"),
).store()
print(f"Project created with id: {project_to_delete.id}")
project_to_delete = project.copy(destination_id=project_to_delete.id)
print(
f"Copied to new project, copied {len(project_to_delete.folders)} folders and {len(project_to_delete.files)} files"
)
# 9) Deleting a project ==============================================================
project_to_delete.delete()
print(f"Project with id: {project_to_delete.id} deleted")
store_project()
Working with folders
"""
Expects that ~/temp exists and is a directory.
The purpose of this script is to demonstrate how to use the new OOP interface for folders.
The following actions are shown in this script:
1. Creating a folder
2. Storing a folder to a project
3. Storing several files to a folder
4. Storing several folders in a folder
5. Getting metadata about a folder and it's immediate children
6. Updating the annotations in bulk for a number of folders and files
7. Deleting a folder
8. Copying a folder
9. Moving a folder
10. Using sync_from_synapse to download the files and folders
"""
import os
from datetime import date, datetime, timedelta, timezone
import synapseclient
from synapseclient.models import File, Folder
PROJECT_ID = "syn52948289"
syn = synapseclient.Synapse(debug=True)
syn.login()
def create_random_file(
path: str,
) -> None:
"""Create a random file with random data.
:param path: The path to create the file at.
"""
with open(path, "wb") as f:
f.write(os.urandom(1))
def try_delete_folder(folder_name: str, parent_id: str) -> None:
"""Simple try catch to delete a folder."""
try:
Folder(name=folder_name, parent_id=parent_id).get().delete()
except Exception:
pass
def store_folder():
# Clean up synapse for previous runs:
try_delete_folder("my_new_folder_for_this_project", PROJECT_ID)
try_delete_folder("destination_for_copy", PROJECT_ID)
try_delete_folder("my_new_folder_for_this_project_I_want_to_delete", PROJECT_ID)
# Creating annotations for my folder ==================================================
annotations_for_my_folder = {
"my_single_key_string": "a",
"my_key_string": ["b", "a", "c"],
"my_key_bool": [False, False, False],
"my_key_double": [1.2, 3.4, 5.6],
"my_key_long": [1, 2, 3],
"my_key_date": [date.today(), date.today() - timedelta(days=1)],
"my_key_datetime": [
datetime.today(),
datetime.today() - timedelta(days=1),
datetime.now(tz=timezone(timedelta(hours=-5))),
datetime(2023, 12, 7, 13, 0, 0, tzinfo=timezone(timedelta(hours=0))),
datetime(2023, 12, 7, 13, 0, 0, tzinfo=timezone(timedelta(hours=-7))),
],
}
# 1) Creating a folder ===============================================================
root_folder_for_my_project = Folder(
name="my_new_folder_for_this_project",
annotations=annotations_for_my_folder,
parent_id=PROJECT_ID,
description="This is a folder with random data.",
)
root_folder_for_my_project = root_folder_for_my_project.store()
print(
f"Folder created: {root_folder_for_my_project.name} with id: {root_folder_for_my_project.id}"
)
# 2) Updating and storing an annotation ==============================================
new_folder_instance = Folder(id=root_folder_for_my_project.id).get()
new_folder_instance.annotations["my_key_string"] = ["new", "values", "here"]
stored_folder = new_folder_instance.store()
print(f"Folder {stored_folder.name} updated with new annotations:")
print(stored_folder.annotations)
# 3) Storing several files to a folder ===============================================
files_to_store = []
for loop in range(1, 10):
name_of_file = f"my_file_with_random_data_{loop}.txt"
path_to_file = os.path.join(os.path.expanduser("~/temp"), name_of_file)
create_random_file(path_to_file)
file = File(
path=path_to_file,
name=name_of_file,
)
files_to_store.append(file)
root_folder_for_my_project.files = files_to_store
root_folder_for_my_project = root_folder_for_my_project.store()
# 4) Storing several folders in a folder =============================================
folders_to_store = []
for loop in range(1, 10):
folder_to_store = Folder(
name=f"my_new_folder_for_this_project_{loop}",
)
folders_to_store.append(folder_to_store)
root_folder_for_my_project.folders = folders_to_store
root_folder_for_my_project = root_folder_for_my_project.store()
# 5) Getting metadata about a folder and it's immediate children =====================
new_folder_instance = Folder(id=root_folder_for_my_project.id).sync_from_synapse(
download_file=False, recursive=False
)
print(f"Synced folder {new_folder_instance.name} from synapse")
for file in new_folder_instance.files:
print(f"Found File in Synapse at: {new_folder_instance.name}/{file.name}")
for folder in new_folder_instance.folders:
print(f"Found Folder in Synapse at: {new_folder_instance.name}/{folder.name}")
# 6) Updating the annotations in bulk for a number of folders and files ==============
new_annotations = {
"my_new_key_string": ["b", "a", "c"],
}
for file in new_folder_instance.files:
file.annotations = new_annotations
for folder in new_folder_instance.folders:
folder.annotations = new_annotations
new_folder_instance.store()
# 7) Deleting a folder ===============================================================
folder_to_delete = Folder(
name="my_new_folder_for_this_project_I_want_to_delete",
parent_id=PROJECT_ID,
).store()
folder_to_delete.delete()
# 8) Copying a folder ===============================================================
destination_folder_to_copy_to = Folder(
name="destination_for_copy", parent_id=PROJECT_ID
).store()
coped_folder = root_folder_for_my_project.copy(
parent_id=destination_folder_to_copy_to.id
)
print(
f"Copied folder from {root_folder_for_my_project.id} to {coped_folder.id} in synapse"
)
# You'll also see all the files/folders were copied too
for file in coped_folder.files:
print(f"Found (copied) File in Synapse at: {coped_folder.name}/{file.name}")
for folder in coped_folder.folders:
print(f"Found (copied) Folder in Synapse at: {coped_folder.name}/{folder.name}")
# 9) Moving a folder ===============================================================
folder_i_am_going_to_move = Folder(
name="folder_i_am_going_to_move", parent_id=PROJECT_ID
).store()
current_parent_id = folder_i_am_going_to_move.parent_id
folder_i_am_going_to_move.parent_id = destination_folder_to_copy_to.id
folder_i_am_going_to_move.store()
print(
f"Moved folder from {current_parent_id} to {folder_i_am_going_to_move.parent_id}"
)
# 10) Using sync_from_synapse to download the files and folders ======================
# This will download all the files and folders in the folder to the local file system
path_to_download = os.path.expanduser("~/temp/recursiveDownload")
if not os.path.exists(path_to_download):
os.mkdir(path_to_download)
root_folder_for_my_project.sync_from_synapse(path=path_to_download)
store_folder()
Working with files
"""
Expects that ~/temp exists and is a directory.
The purpose of this script is to demonstrate how to use the new OOP interface for files.
The following actions are shown in this script:
1. Creating a file
2. Storing a file
3. Storing a file in a sub-folder
4. Renaming a file
5. Downloading a file
6. Deleting a file
7. Copying a file
8. Storing an activity to a file
9. Retrieve an activity from a file
"""
import os
from datetime import date, datetime, timedelta, timezone
import synapseclient
from synapseclient.core import utils
from synapseclient.models import Activity, File, Folder, UsedEntity, UsedURL
PROJECT_ID = "syn52948289"
syn = synapseclient.Synapse(debug=True)
syn.login()
def create_random_file(
path: str,
) -> None:
"""Create a random file with random data.
:param path: The path to create the file at.
"""
with open(path, "wb") as f:
f.write(os.urandom(1))
def store_file():
# Cleanup synapse for previous runs - Does not delete local files/directories:
try:
Folder(name="file_script_folder", parent_id=PROJECT_ID).get().delete()
except Exception:
pass
if not os.path.exists(os.path.expanduser("~/temp/myNewFolder")):
os.mkdir(os.path.expanduser("~/temp/myNewFolder"))
script_file_folder = Folder(name="file_script_folder", parent_id=PROJECT_ID).store()
# Creating annotations for my file ==================================================
annotations_for_my_file = {
"my_single_key_string": "a",
"my_key_string": ["b", "a", "c"],
"my_key_bool": [False, False, False],
"my_key_double": [1.2, 3.4, 5.6],
"my_key_long": [1, 2, 3],
"my_key_date": [date.today(), date.today() - timedelta(days=1)],
"my_key_datetime": [
datetime.today(),
datetime.today() - timedelta(days=1),
datetime.now(tz=timezone(timedelta(hours=-5))),
datetime(2023, 12, 7, 13, 0, 0, tzinfo=timezone(timedelta(hours=0))),
datetime(2023, 12, 7, 13, 0, 0, tzinfo=timezone(timedelta(hours=-7))),
],
}
name_of_file = "file_script_my_file_with_random_data.txt"
path_to_file = os.path.join(os.path.expanduser("~/temp"), name_of_file)
create_random_file(path_to_file)
# 1. Creating a file =================================================================
file = File(
path=path_to_file,
annotations=annotations_for_my_file,
parent_id=script_file_folder.id,
description="This is a file with random data.",
)
# 2. Storing a file ==================================================================
file = file.store()
print(f"File created: ID: {file.id}, Parent ID: {file.parent_id}")
name_of_file = "file_in_a_sub_folder.txt"
path_to_file = os.path.join(os.path.expanduser("~/temp"), name_of_file)
create_random_file(path_to_file)
# 3. Storing a file to a sub-folder ==================================================
script_sub_folder = Folder(
name="file_script_sub_folder", parent_id=script_file_folder.id
).store()
file_in_a_sub_folder = File(
path=path_to_file,
annotations=annotations_for_my_file,
parent_id=script_sub_folder.id,
description="This is a file with random data.",
)
file_in_a_sub_folder = file_in_a_sub_folder.store()
print(
f"File created in sub folder: ID: {file_in_a_sub_folder.id}, Parent ID: {file_in_a_sub_folder.parent_id}"
)
# 4. Renaming a file =================================================================
name_of_file = "file_script_my_file_to_rename.txt"
path_to_file = os.path.join(os.path.expanduser("~/temp"), name_of_file)
create_random_file(path_to_file)
# The name of the entity, and the name of the file is disjointed.
# For example, the name of the file is "file_script_my_file_to_rename.txt"
# and the name of the entity is "this_name_is_different"
file: File = File(
path=path_to_file,
name="this_name_is_different",
parent_id=script_file_folder.id,
).store()
print(f"File created with name: {file.name}")
print(f"The path of the file is: {file.path}")
# You can change the name of the entity without changing the name of the file.
file.name = "modified_name_attribute"
file.store()
print(f"File renamed to: {file.name}")
# You can then change the name of the file that would be downloaded like:
file.change_metadata(download_as="new_name_for_downloading.txt")
print(f"File download values changed to: {file.file_handle.file_name}")
# 5. Downloading a file ===============================================================
# Downloading a file to a location has a default beahvior of "keep.both"
downloaded_file = File(
id=file.id, path=os.path.expanduser("~/temp/myNewFolder")
).get()
print(f"Downloaded file: {downloaded_file.path}")
# I can also specify how collisions are handled when downloading a file.
# This will replace the file on disk if it already exists and is different (after).
path_to_file = downloaded_file.path
create_random_file(path_to_file)
print(f"Before file md5: {utils.md5_for_file(path_to_file).hexdigest()}")
downloaded_file = File(
id=downloaded_file.id,
path=os.path.expanduser("~/temp/myNewFolder"),
if_collision="overwrite.local",
).get()
print(f"After file md5: {utils.md5_for_file(path_to_file).hexdigest()}")
# This will keep the file on disk (before), and no file is downloaded
path_to_file = downloaded_file.path
create_random_file(path_to_file)
print(f"Before file md5: {utils.md5_for_file(path_to_file).hexdigest()}")
downloaded_file = File(
id=downloaded_file.id,
path=os.path.expanduser("~/temp/myNewFolder"),
if_collision="keep.local",
).get()
print(f"After file md5: {utils.md5_for_file(path_to_file).hexdigest()}")
# 6. Deleting a file =================================================================
# Suppose I have a file that I want to delete.
name_of_file = "file_to_delete.txt"
path_to_file = os.path.join(os.path.expanduser("~/temp"), name_of_file)
create_random_file(path_to_file)
file_to_delete = File(path=path_to_file, parent_id=script_file_folder.id).store()
file_to_delete.delete()
# 7. Copying a file ===================================================================
print(
f"File I am going to copy: ID: {file_in_a_sub_folder.id}, Parent ID: {file_in_a_sub_folder.parent_id}"
)
new_sub_folder = Folder(
name="sub_sub_folder", parent_id=script_file_folder.id
).store()
copied_file_instance = file_in_a_sub_folder.copy(parent_id=new_sub_folder.id)
print(
f"File I copied: ID: {copied_file_instance.id}, Parent ID: {copied_file_instance.parent_id}"
)
# 8. Storing an activity to a file =====================================================
activity = Activity(
name="some_name",
description="some_description",
used=[
UsedURL(name="example", url="https://www.synapse.org/"),
UsedEntity(target_id="syn456", target_version_number=1),
],
executed=[
UsedURL(name="example", url="https://www.synapse.org/"),
UsedEntity(target_id="syn789", target_version_number=1),
],
)
name_of_file = "file_with_an_activity.txt"
path_to_file = os.path.join(os.path.expanduser("~/temp"), name_of_file)
create_random_file(path_to_file)
file_with_activity = File(
path=path_to_file, parent_id=script_file_folder.id, activity=activity
).store()
print(file_with_activity.activity)
# 9. When I am retrieving that file later on I can get the activity like =============
# By also specifying download_file=False, I can get the activity without downloading the file.
new_file_with_activity_instance = File(
id=file_with_activity.id, download_file=False
).get(include_activity=True)
print(new_file_with_activity_instance.activity)
store_file()
Working with tables
"""The purpose of this script is to demonstrate how to use the new OOP interface for tables.
The following actions are shown in this script:
1. Creating a table
2. Storing a table
3. Getting a table
4. Storing rows in a table
5. Querying for data from a table
6. Deleting a row from a table
7. Deleting a table
"""
import csv
import os
import random
import string
from datetime import date, datetime, timedelta, timezone
import synapseclient
from synapseclient.models import Column, ColumnType, CsvResultFormat, Row, Table
PROJECT_ID = "syn52948289"
syn = synapseclient.Synapse(debug=True)
syn.login()
def write_random_csv_with_data(path: str):
randomized_data_columns = {
"my_string_column": str,
"my_integer_column": int,
"my_double_column": float,
"my_boolean_column": bool,
}
# Generate randomized data
data = {}
for name, type in randomized_data_columns.items():
if type == int:
data[name] = [random.randint(0, 100) for _ in range(10)]
elif type == float:
data[name] = [random.uniform(0, 100) for _ in range(10)]
elif type == bool:
data[name] = [bool(random.getrandbits(1)) for _ in range(10)]
elif type == str:
data[name] = [
"".join(random.choices(string.ascii_uppercase + string.digits, k=5))
for _ in range(10)
]
with open(path, "w", newline="", encoding="utf-8") as csvfile:
writer = csv.writer(csvfile)
# Write column names
writer.writerow(data.keys())
# Write data
for i in range(10):
writer.writerow([values[i] for values in data.values()])
def store_table():
# Creating annotations for my table ==================================================
annotations_for_my_table = {
"my_single_key_string": "a",
"my_key_string": ["b", "a", "c"],
"my_key_bool": [False, False, False],
"my_key_double": [1.2, 3.4, 5.6],
"my_key_long": [1, 2, 3],
"my_key_date": [date.today(), date.today() - timedelta(days=1)],
"my_key_datetime": [
datetime.today(),
datetime.today() - timedelta(days=1),
datetime.now(tz=timezone(timedelta(hours=-5))),
datetime(2023, 12, 7, 13, 0, 0, tzinfo=timezone(timedelta(hours=0))),
datetime(2023, 12, 7, 13, 0, 0, tzinfo=timezone(timedelta(hours=-7))),
],
}
# Creating columns for my table ======================================================
columns = [
Column(id=None, name="my_string_column", column_type=ColumnType.STRING),
Column(id=None, name="my_integer_column", column_type=ColumnType.INTEGER),
Column(id=None, name="my_double_column", column_type=ColumnType.DOUBLE),
Column(id=None, name="my_boolean_column", column_type=ColumnType.BOOLEAN),
]
# Creating a table ===============================================================
table = Table(
name="my_first_test_table",
columns=columns,
parent_id=PROJECT_ID,
annotations=annotations_for_my_table,
)
table = table.store_schema()
print("Table created:")
print(table)
# Getting a table =================================================================
copy_of_table = Table(id=table.id)
copy_of_table = copy_of_table.get()
print("Table retrieved:")
print(copy_of_table)
# Updating annotations on my table ===============================================
copy_of_table.annotations["my_key_string"] = ["new", "values", "here"]
stored_table = copy_of_table.store_schema()
print("Table updated:")
print(stored_table)
# Storing data to a table =========================================================
name_of_csv = "my_csv_file_with_random_data"
path_to_csv = os.path.join(os.path.expanduser("~/temp"), f"{name_of_csv}.csv")
write_random_csv_with_data(path_to_csv)
csv_path = copy_of_table.store_rows_from_csv(csv_path=path_to_csv)
print("Stored data to table from CSV:")
print(csv_path)
# Querying for data from a table =================================================
destination_csv_location = os.path.expanduser("~/temp/my_query_results")
table_id_to_query = copy_of_table.id
Table.query(
query=f"SELECT * FROM {table_id_to_query}",
result_format=CsvResultFormat(download_location=destination_csv_location),
)
print(f"Created results at: {destination_csv_location}")
# Deleting rows from a table =====================================================
copy_of_table.delete_rows(rows=[Row(row_id=1)])
# Deleting a table ===============================================================
table_to_delete = Table(
name="my_test_table_I_want_to_delete",
columns=columns,
parent_id=PROJECT_ID,
).store_schema()
table_to_delete.delete()
store_table()
Current Synapse interface for working with a project
"""The purpose of this script is to demonstrate how to use the current synapse interface for projects.
The following actions are shown in this script:
1. Creating a project
2. Getting metadata about a project
3. Storing several files to a project
4. Storing several folders in a project with a file in each folder
5. Updating the annotations in bulk for a number of folders and files
6. Using synapseutils to sync a project from and to synapse
7. Deleting a project
All steps also include setting a number of annotations for the objects.
"""
import os
import uuid
from datetime import datetime, timedelta, timezone
import synapseclient
import synapseutils
from synapseclient import Annotations, File, Folder, Project
syn = synapseclient.Synapse(debug=True)
syn.login()
def create_random_file(
path: str,
) -> None:
"""Create a random file with random data.
:param path: The path to create the file at.
"""
with open(path, "wb") as f:
f.write(os.urandom(1))
# Creating annotations for my project ==================================================
my_annotations_dict = {
"my_key_string": ["b", "a", "c"],
"my_key_bool": [False, False, False],
"my_key_double": [1.2, 3.4, 5.6],
"my_key_long": [1, 2, 3],
"my_key_timestamp": [
datetime.today(),
datetime.today() - timedelta(days=1),
datetime.now(tz=timezone(timedelta(hours=-5))),
datetime(2023, 12, 7, 13, 0, 0, tzinfo=timezone(timedelta(hours=0))),
datetime(2023, 12, 7, 13, 0, 0, tzinfo=timezone(timedelta(hours=-7))),
],
}
# Creating a project =====================================================================
project = Project(
name="my_new_project_for_testing_synapse_client",
annotations=my_annotations_dict,
description="This is a project with random data.",
)
my_stored_project: Project = syn.store(project)
print(my_stored_project)
# Getting metadata about a project =======================================================
my_project = syn.get(entity=my_stored_project.id)
print(my_project)
# Storing several files to a project =====================================================
for loop in range(1, 10):
name_of_file = f"my_file_with_random_data_{loop}.txt"
path_to_file = os.path.join(os.path.expanduser("~/temp"), name_of_file)
create_random_file(path_to_file)
# Creating and uploading a file to a project =====================================
file = File(
path=path_to_file,
name=name_of_file,
parent=my_stored_project.id,
)
my_stored_file = syn.store(obj=file)
my_annotations = Annotations(
id=my_stored_file.id,
etag=my_stored_file.etag,
**my_annotations_dict,
)
syn.set_annotations(annotations=my_annotations)
# Storing several folders to a project ===================================================
for loop in range(1, 10):
# Creating and uploading a folder to a project ===================================
folder = Folder(
name=f"my_folder_{loop}",
parent=my_stored_project.id,
)
my_stored_folder = syn.store(obj=folder)
my_annotations = Annotations(
id=my_stored_folder.id,
etag=my_stored_folder.etag,
**my_annotations_dict,
)
syn.set_annotations(annotations=my_annotations)
# Adding a file to a folder ======================================================
name_of_file = f"my_file_with_random_data_{uuid.uuid4()}.txt"
path_to_file = os.path.join(os.path.expanduser("~/temp"), name_of_file)
create_random_file(path_to_file)
file = File(
path=path_to_file,
name=name_of_file,
parent=my_stored_folder.id,
)
my_stored_file = syn.store(obj=file)
my_annotations = Annotations(
id=my_stored_file.id,
etag=my_stored_file.etag,
**my_annotations_dict,
)
syn.set_annotations(annotations=my_annotations)
# Updating the annotations in bulk for a number of folders and files =====================
new_annotations = {
"my_key_string": ["bbbbb", "aaaaa", "ccccc"],
}
# Note: This `getChildren` function will only return the items that are directly
# under the `parent`. You would need to recursively call this function to get all
# of the children for all folders under the parent.
for child in syn.getChildren(
parent=my_stored_project.id, includeTypes=["folder", "file"]
):
is_folder = (
"type" in child and child["type"] == "org.sagebionetworks.repo.model.Folder"
)
is_file = (
"type" in child and child["type"] == "org.sagebionetworks.repo.model.FileEntity"
)
if is_folder:
my_folder = syn.get(entity=child["id"])
new_saved_annotations = syn.set_annotations(
Annotations(id=child["id"], etag=my_folder.etag, **new_annotations)
)
print(new_saved_annotations)
elif is_file:
my_file = syn.get(entity=child["id"], downloadFile=False)
new_saved_annotations = syn.set_annotations(
Annotations(id=child["id"], etag=my_file.etag, **new_annotations)
)
print(new_saved_annotations)
# Using synapseutils to sync a project from and to synapse ===============================
# This `syncFromSynapse` will download all files and folders under the project.
# In addition it creates a manifest TSV file that contains the metadata for all
# of the files and folders under the project.
project_download_location = os.path.expanduser("~/my_synapse_project")
result = synapseutils.syncFromSynapse(
syn=syn, entity=my_stored_project, path=project_download_location
)
print(result)
# This `syncToSynapse` will upload all files and folders under the project that
# are defined in the manifest TSV file.
# ---
# 12/08/2023 note: There is a bug in the `syncToSynapse` method if you are using
# multiple annotations for a single key. This will be fixed in the next few releases.
# Track https://sagebionetworks.jira.com/browse/SYNPY-1357 for more information.
synapseutils.syncToSynapse(
syn,
manifestFile=f"{project_download_location}/SYNAPSE_METADATA_MANIFEST.tsv",
sendMessages=False,
)
# Creating and then deleting a project ===================================================
project = Project(
name="my_new_project_for_testing_synapse_client_that_will_be_deleted",
annotations=my_annotations_dict,
description="This is a project with random data.",
)
my_stored_project: Project = syn.store(project)
syn.delete(obj=my_stored_project.id)
Working with activities
"""The purpose of this script is to demonstrate how to use the OOP interface for Activity.
The following actions are shown in this script:
1. Creating a file with an Activity
2. Retrieve an activity by parent File
3. Creating a second file with the same activity
4. Modifying the activity attached to both Files
5. Creating a table with an Activity
"""
import os
import synapseclient
from synapseclient.models import (
Activity,
Column,
ColumnType,
File,
Table,
UsedEntity,
UsedURL,
)
PROJECT_ID = "syn52948289"
syn = synapseclient.Synapse(debug=True)
syn.login()
def create_random_file(
path: str,
) -> None:
"""Create a random file with random data.
Arguments:
path: The path to create the file at.
"""
with open(path, "wb") as f:
f.write(os.urandom(1))
def store_activity_on_file():
name_of_file = "my_file_with_random_data.txt"
path_to_file = os.path.join(os.path.expanduser("~/temp"), name_of_file)
create_random_file(path_to_file)
name_of_second_file = "my_second_file_with_random_data.txt"
path_to_second_file = os.path.join(
os.path.expanduser("~/temp"), name_of_second_file
)
create_random_file(path_to_second_file)
# Create an activity =================================================================
activity = Activity(
name="My Activity",
description="This is an activity.",
used=[
UsedURL(name="Used URL", url="https://www.synapse.org/"),
UsedEntity(target_id=PROJECT_ID),
],
executed=[
UsedURL(name="Used URL", url="https://www.synapse.org/"),
UsedEntity(target_id=PROJECT_ID),
],
)
# Creating and uploading a file to a project =========================================
file = File(
path=path_to_file,
name=name_of_file,
parent_id=PROJECT_ID,
description="This is a file with random data.",
activity=activity,
)
file = file.store()
print("File created with activity:")
print(activity)
activity_copy = Activity.from_parent(parent=file)
# Storing a second file to a project and re-use the activity =========================
second_file = File(
path=path_to_second_file,
name=name_of_second_file,
parent_id=PROJECT_ID,
description="This is a file with random data.",
activity=activity_copy,
)
second_file.store()
print("Second file created with activity:")
print(second_file.activity)
# # Update the already created activity, which updates the activity on both files ====
new_activity_instance = Activity(
# In order to update an existing activity you must provide the id and etag.
id=second_file.activity.id,
etag=second_file.activity.etag if second_file.activity else None,
name="My Activity - MODIFIED",
used=[
UsedURL(name="Used URL", url="https://www.synapse.org/"),
UsedEntity(target_id=PROJECT_ID),
],
executed=[
UsedURL(name="Used URL", url="https://www.synapse.org/"),
UsedEntity(target_id=PROJECT_ID),
],
)
# These 3 will be the same activity
print("Modified activity showing name is updated for all files:")
print(new_activity_instance.store().name)
print(Activity.from_parent(parent=file).name)
print(Activity.from_parent(parent=second_file).name)
def store_activity_on_table():
# Create an activity =================================================================
activity = Activity(
name="My Activity",
description="This is an activity.",
used=[
UsedURL(name="Used URL", url="https://www.synapse.org/"),
UsedEntity(target_id=PROJECT_ID),
],
executed=[
UsedURL(name="Used URL", url="https://www.synapse.org/"),
UsedEntity(target_id=PROJECT_ID),
],
)
# Creating columns for my table ======================================================
columns = [
Column(id=None, name="my_string_column", column_type=ColumnType.STRING),
]
# Creating a table ===============================================================
table = Table(
name="my_first_test_table",
columns=columns,
parent_id=PROJECT_ID,
activity=activity,
)
table = table.store_schema()
print("Table created with activity:")
print(table.activity)
store_activity_on_file()
store_activity_on_table()
Working with teams
"""The purpose of this script is to demonstrate how to use the new OOP interface for teams.
The following actions are shown in this script:
1. Creating a Team
2. Instantiating a Team object from Synapse
3. Getting information about the members of a Team
4. Inviting a user to a Team
5. Checking on invitations to join a Team
6. Deleting a Team
"""
import time
import synapseclient
from synapseclient.models.team import Team
syn = synapseclient.Synapse(debug=True)
syn.login()
def new_team():
# Create a team
new_team = Team(
name="python-client-test-team",
description="testing OOP interface",
can_public_join=False,
)
my_synapse_team = new_team.create()
print(my_synapse_team)
# Instantiate a Team object from a Synapse team
my_team = Team.from_id(id=my_synapse_team.id)
print(my_team)
# Sleep because the API for retrieving a team by name is eventually consistent. from_id works right away, however.
time.sleep(5)
my_team = Team.from_name(name=my_synapse_team.name)
print(my_team)
# Refresh the team to get the latest information
my_team.get()
print(my_team)
# Get information about the members of a Team
members = my_team.members()
print(members)
# Invite a user to a Team
invite = my_team.invite(
user="test_account_synapse_client",
message="testing OOP interface (do not accept)",
)
print(invite)
# Get open invitations for the Team
invitations = my_team.open_invitations()
print(invitations)
# Delete the Team
my_team.delete()
new_team()
API reference¶
dataclass
¶
Bases: ProjectSynchronousProtocol, AccessControllable, StorableContainer
A Project is a top-level container for organizing data in Synapse.
| ATTRIBUTE | DESCRIPTION |
|---|---|
id |
The unique immutable ID for this project. A new ID will be generated for new Projects. Once issued, this ID is guaranteed to never change or be re-issued |
name |
The name of this project. Must be 256 characters or less. Names may only contain: letters, numbers, spaces, underscores, hyphens, periods, plus signs, apostrophes, and parentheses |
description |
The description of this entity. Must be 1000 characters or less. |
etag |
Synapse employs an Optimistic Concurrency Control (OCC) scheme to handle concurrent updates. Since the E-Tag changes every time an entity is updated it is used to detect when a client's current representation of an entity is out-of-date. |
created_on |
The date this entity was created. |
modified_on |
The date this entity was last modified. |
created_by |
The ID of the user that created this entity. |
modified_by |
The ID of the user that last modified this entity. |
alias |
The project alias for use in friendly project urls. |
files |
Any files that are at the root directory of the project. |
folders |
Any folders that are at the root directory of the project. |
annotations |
Additional metadata associated with the folder. The key is the name
of your desired annotations. The value is an object containing a list of
values (use empty list to represent no values for key) and the value type
associated with all values in the list. To remove all annotations set this
to an empty dict
TYPE:
|
create_or_update |
(Store only) Indicates whether the method should automatically perform an update if the resource conflicts with an existing Synapse object. When True this means that any changes to the resource will be non-destructive. This boolean is ignored if you've already stored or retrieved the resource
from Synapse for this instance at least once. Any changes to the resource
will be destructive in this case. For example if you want to delete the
content for a field you will need to call
TYPE:
|
parent_id |
The parent ID of the project. In practice projects do not have a parent, but this is required for the inner workings of Synapse. |
Creating a project
This example shows how to create a project
from synapseclient.models import Project, File
import synapseclient
synapseclient.login()
my_annotations = {
"my_single_key_string": "a",
"my_key_string": ["b", "a", "c"],
}
project = Project(
name="My unique project name",
annotations=my_annotations,
description="This is a project with random data.",
)
project = project.store()
print(project)
Storing several files to a project
This example shows how to store several files to a project
file_1 = File(
path=path_to_file_1,
name=name_of_file_1,
)
file_2 = File(
path=path_to_file_2,
name=name_of_file_2,
)
project.files = [file_1, file_2]
project = project.store()
Source code in synapseclient/models/project.py
26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 | |
Functions¶
Get the project metadata from Synapse.
| PARAMETER | DESCRIPTION |
|---|---|
synapse_client
|
If not passed in and caching was not disabled by
|
| RETURNS | DESCRIPTION |
|---|---|
Project
|
The project object. |
Using this method
Retrieve the project from Synapse using ID
project = Project(id="syn123").get()
Retrieve the project from Synapse using Name
project = Project(name="my_project").get()
| RAISES | DESCRIPTION |
|---|---|
ValueError
|
If the project ID or Name is not set. |
SynapseNotFoundError
|
If the project is not found in Synapse. |
Source code in synapseclient/models/protocols/project_protocol.py
60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 | |
store(failure_strategy: FailureStrategy = LOG_EXCEPTION, *, synapse_client: Optional[Synapse] = None) -> Project
Store project, files, and folders to synapse. If you have any files or folders
attached to this project they will be stored as well. You may attach files
and folders to this project by setting the files and folders attributes.
By default the store operation will non-destructively update the project if
you have not already retrieved the project from Synapse. If you have already
retrieved the project from Synapse then the store operation will be destructive
and will overwrite the project with the current state of this object. See the
create_or_update attribute for more information.
| PARAMETER | DESCRIPTION |
|---|---|
failure_strategy
|
Determines how to handle failures when storing attached Files and Folders under this Project and an exception occurs.
TYPE:
|
synapse_client
|
If not passed in and caching was not disabled by
|
| RETURNS | DESCRIPTION |
|---|---|
Project
|
The project object. |
Using this method to update the description
Store the project to Synapse using ID
project = Project(id="syn123", description="new").store()
Store the project to Synapse using Name
project = Project(name="my_project", description="new").store()
| RAISES | DESCRIPTION |
|---|---|
ValueError
|
If the project name is not set. |
Source code in synapseclient/models/protocols/project_protocol.py
19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 | |
Delete the project from Synapse.
| PARAMETER | DESCRIPTION |
|---|---|
synapse_client
|
If not passed in and caching was not disabled by
|
| RETURNS | DESCRIPTION |
|---|---|
None
|
None |
Using this method
Delete the project from Synapse using ID
Project(id="syn123").delete()
Delete the project from Synapse using Name
Project(name="my_project").delete()
| RAISES | DESCRIPTION |
|---|---|
ValueError
|
If the project ID or Name is not set. |
SynapseNotFoundError
|
If the project is not found in Synapse. |
Source code in synapseclient/models/protocols/project_protocol.py
91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 | |
sync_from_synapse(path: Optional[str] = None, recursive: bool = True, download_file: bool = True, if_collision: str = COLLISION_OVERWRITE_LOCAL, failure_strategy: FailureStrategy = LOG_EXCEPTION, *, synapse_client: Optional[Synapse] = None) -> Self
Sync this container and all possible sub-folders from Synapse. By default this
will download the files that are found and it will populate the
files and folders attributes with the found files and folders. If you only
want to retrieve the full tree of metadata about your container specify
download_file as False.
This works similar to synapseutils.syncFromSynapse, however, this does not currently support the writing of data to a manifest TSV file. This will be a future enhancement.
Only Files and Folders are supported at this time to be synced from synapse.
| PARAMETER | DESCRIPTION |
|---|---|
path
|
An optional path where the file hierarchy will be reproduced. If not specified the files will by default be placed in the synapseCache. |
recursive
|
Whether or not to recursively get the entire hierarchy of the folder and sub-folders.
TYPE:
|
download_file
|
Whether to download the files found or not.
TYPE:
|
if_collision
|
Determines how to handle file collisions. May be
TYPE:
|
failure_strategy
|
Determines how to handle failures when retrieving children under this Folder and an exception occurs.
TYPE:
|
synapse_client
|
If not passed in and caching was not disabled by
|
| RETURNS | DESCRIPTION |
|---|---|
Self
|
The object that was called on. This will be the same object that was called on to start the sync. |
Using this function
Suppose I want to walk the immediate children of a folder without downloading the files:
from synapseclient import Synapse
from synapseclient.models import Folder
syn = Synapse()
syn.login()
my_folder = Folder(id="syn12345")
my_folder.sync_from_synapse(download_file=False, recursive=False)
for folder in my_folder.folders:
print(folder.name)
for file in my_folder.files:
print(file.name)
Suppose I want to download the immediate children of a folder:
from synapseclient import Synapse
from synapseclient.models import Folder
syn = Synapse()
syn.login()
my_folder = Folder(id="syn12345")
my_folder.sync_from_synapse(path="/path/to/folder", recursive=False)
for folder in my_folder.folders:
print(folder.name)
for file in my_folder.files:
print(file.name)
Suppose I want to download the immediate all children of a Project and all sub-folders and files:
from synapseclient import Synapse
from synapseclient.models import Project
syn = Synapse()
syn.login()
my_project = Project(id="syn12345")
my_project.sync_from_synapse(path="/path/to/folder")
| RAISES | DESCRIPTION |
|---|---|
ValueError
|
If the folder does not have an id set. |
A sequence diagram for this method is as follows:
sequenceDiagram
autonumber
participant project_or_folder
activate project_or_folder
project_or_folder->>sync_from_synapse: Recursive search and download files
activate sync_from_synapse
opt Current instance not retrieved from Synapse
sync_from_synapse->>project_or_folder: Call `.get()` method
project_or_folder-->>sync_from_synapse: .
end
loop For each return of the generator
sync_from_synapse->>client: call `.getChildren()` method
client-->>sync_from_synapse: .
note over sync_from_synapse: Append to a running list
end
loop For each child
note over sync_from_synapse: Create all `pending_tasks` at current depth
alt Child is File
note over sync_from_synapse: Append `file.get()` method
else Child is Folder
note over sync_from_synapse: Append `folder.get()` method
alt Recursive is True
note over sync_from_synapse: Append `folder.sync_from_synapse()` method
end
end
end
loop For each task in pending_tasks
par `file.get()`
sync_from_synapse->>File: Retrieve File metadata and Optionally download
File->>client: `.get()`
client-->>File: .
File-->>sync_from_synapse: .
and `folder.get()`
sync_from_synapse->>Folder: Retrieve Folder metadataa
Folder->>client: `.get()`
client-->>Folder: .
Folder-->>sync_from_synapse: .
and `folder.sync_from_synapse()`
note over sync_from_synapse: This is a recursive call to `sync_from_synapse`
sync_from_synapse->>sync_from_synapse: Recursive call to `.sync_from_synapse()`
end
end
deactivate sync_from_synapse
deactivate project_or_folderSource code in synapseclient/models/protocols/storable_container_protocol.py
19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 | |
get_permissions(*, synapse_client: Optional[Synapse] = None) -> Permissions
Get the permissions that the caller has on an Entity.
| PARAMETER | DESCRIPTION |
|---|---|
synapse_client
|
If not passed in and caching was not disabled by
|
| RETURNS | DESCRIPTION |
|---|---|
Permissions
|
A Permissions object |
Using this function:
Getting permissions for a Synapse Entity
permissions = File(id="syn123").get_permissions()
Getting access types list from the Permissions object
permissions.access_types
Source code in synapseclient/models/protocols/access_control_protocol.py
18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 | |
Get the ACL that a user or group has on an Entity.
| PARAMETER | DESCRIPTION |
|---|---|
principal_id
|
Identifier of a user or group (defaults to PUBLIC users)
TYPE:
|
synapse_client
|
If not passed in and caching was not disabled by
|
| RETURNS | DESCRIPTION |
|---|---|
List[str]
|
An array containing some combination of ['READ', 'UPDATE', 'CREATE', 'DELETE', 'DOWNLOAD', 'MODERATE', 'CHANGE_PERMISSIONS', 'CHANGE_SETTINGS'] or an empty array |
Source code in synapseclient/models/protocols/access_control_protocol.py
47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 | |
set_permissions(principal_id: int = None, access_type: List[str] = None, modify_benefactor: bool = False, warn_if_inherits: bool = True, overwrite: bool = True, *, synapse_client: Optional[Synapse] = None) -> Dict[str, Union[str, list]]
Sets permission that a user or group has on an Entity. An Entity may have its own ACL or inherit its ACL from a benefactor.
| PARAMETER | DESCRIPTION |
|---|---|
principal_id
|
Identifier of a user or group.
TYPE:
|
access_type
|
Type of permission to be granted. One or more of CREATE, READ, DOWNLOAD, UPDATE, DELETE, CHANGE_PERMISSIONS. Defaults to ['READ', 'DOWNLOAD'] |
modify_benefactor
|
Set as True when modifying a benefactor's ACL
TYPE:
|
warn_if_inherits
|
Set as False, when creating a new ACL. Trying to modify the ACL of an Entity that inherits its ACL will result in a warning
TYPE:
|
overwrite
|
By default this function overwrites existing permissions for the specified user. Set this flag to False to add new permissions non-destructively.
TYPE:
|
synapse_client
|
If not passed in and caching was not disabled by
|
| RETURNS | DESCRIPTION |
|---|---|
Dict[str, Union[str, list]]
|
An Access Control List object |
Setting permissions
Grant all registered users download access
File(id="syn123").set_permissions(principal_id=273948, access_type=['READ','DOWNLOAD'])
Grant the public view access
File(id="syn123").set_permissions(principal_id=273949, access_type=['READ'])
Source code in synapseclient/models/protocols/access_control_protocol.py
68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 | |
dataclass
¶
Bases: FolderSynchronousProtocol, AccessControllable, StorableContainer
Folder is a hierarchical container for organizing data in Synapse.
| ATTRIBUTE | DESCRIPTION |
|---|---|
id |
The unique immutable ID for this folder. A new ID will be generated for new Folders. Once issued, this ID is guaranteed to never change or be re-issued. |
name |
The name of this folder. Must be 256 characters or less. Names may only contain: letters, numbers, spaces, underscores, hyphens, periods, plus signs, apostrophes, and parentheses. |
parent_id |
The ID of the Project or Folder that is the parent of this Folder. |
description |
The description of this entity. Must be 1000 characters or less. |
etag |
(Read Only) Synapse employs an Optimistic Concurrency Control (OCC) scheme to handle concurrent updates. Since the E-Tag changes every time an entity is updated it is used to detect when a client's current representation of an entity is out-of-date. |
created_on |
(Read Only) The date this entity was created. |
modified_on |
(Read Only) The date this entity was last modified. |
created_by |
(Read Only) The ID of the user that created this entity. |
modified_by |
(Read Only) The ID of the user that last modified this entity. |
files |
Files that exist within this folder. |
folders |
Folders that exist within this folder. |
annotations |
Additional metadata associated with the folder. The key is the name
of your desired annotations. The value is an object containing a list of
values (use empty list to represent no values for key) and the value type
associated with all values in the list. To remove all annotations set this
to an empty dict
TYPE:
|
create_or_update |
(Store only) Indicates whether the method should automatically perform an update if the resource conflicts with an existing Synapse object. When True this means that any changes to the resource will be non-destructive. This boolean is ignored if you've already stored or retrieved the resource
from Synapse for this instance at least once. Any changes to the resource
will be destructive in this case. For example if you want to delete the
content for a field you will need to call
TYPE:
|
Source code in synapseclient/models/folder.py
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Functions¶
get(parent: Optional[Union[Folder, Project]] = None, *, synapse_client: Optional[Synapse] = None) -> Folder
Get the folder metadata from Synapse. You are able to find a folder by either the id or the name and parent_id.
| PARAMETER | DESCRIPTION |
|---|---|
parent
|
The parent folder or project this folder exists under. |
synapse_client
|
If not passed in and caching was not disabled by
|
| RETURNS | DESCRIPTION |
|---|---|
Folder
|
The folder object. |
| RAISES | DESCRIPTION |
|---|---|
ValueError
|
If the folder does not have an id or a
(name and ( |
Source code in synapseclient/models/protocols/folder_protocol.py
53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 | |
store(parent: Optional[Union[Folder, Project]] = None, failure_strategy: FailureStrategy = LOG_EXCEPTION, *, synapse_client: Optional[Synapse] = None) -> Folder
Store folders and files to synapse. If you have any files or folders attached
to this folder they will be stored as well. You may attach files and folders
to this folder by setting the files and folders attributes.
By default the store operation will non-destructively update the folder if
you have not already retrieved the folder from Synapse. If you have already
retrieved the folder from Synapse then the store operation will be destructive
and will overwrite the folder with the current state of this object. See the
create_or_update attribute for more information.
| PARAMETER | DESCRIPTION |
|---|---|
parent
|
The parent folder or project to store the folder in. |
failure_strategy
|
Determines how to handle failures when storing attached Files and Folders under this Folder and an exception occurs.
TYPE:
|
synapse_client
|
If not passed in and caching was not disabled by
|
| RETURNS | DESCRIPTION |
|---|---|
Folder
|
The folder object. |
| RAISES | DESCRIPTION |
|---|---|
ValueError
|
If the folder does not have an id or a
(name and ( |
Source code in synapseclient/models/protocols/folder_protocol.py
19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 | |
Delete the folder from Synapse by its id.
| PARAMETER | DESCRIPTION |
|---|---|
synapse_client
|
If not passed in and caching was not disabled by
|
| RETURNS | DESCRIPTION |
|---|---|
None
|
None |
| RAISES | DESCRIPTION |
|---|---|
ValueError
|
If the folder does not have an id set. |
Source code in synapseclient/models/protocols/folder_protocol.py
77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 | |
copy(parent_id: str, copy_annotations: bool = True, exclude_types: Optional[List[str]] = None, file_update_existing: bool = False, file_copy_activity: Union[str, None] = 'traceback', *, synapse_client: Optional[Synapse] = None) -> Folder
Copy the folder to another Synapse location. This will recursively copy all Tables, Links, Files, and Folders within the folder.
| PARAMETER | DESCRIPTION |
|---|---|
parent_id
|
Synapse ID of a folder/project that the copied entity is being copied to
TYPE:
|
copy_annotations
|
True to copy the annotations.
TYPE:
|
exclude_types
|
A list of entity types ['file', 'table', 'link'] which determines which entity types to not copy. Defaults to an empty list. |
file_update_existing
|
When the destination has a file that has the same name, users can choose to update that file.
TYPE:
|
file_copy_activity
|
Has three options to set the activity of the copied file: |
synapse_client
|
If not passed in and caching was not disabled by
|
| RETURNS | DESCRIPTION |
|---|---|
Folder
|
The copied folder object. |
Using this function
Assuming you have a folder with the ID "syn123" and you want to copy it to a project with the ID "syn456":
new_folder_instance = await Folder(id="syn123").copy(parent_id="syn456")
Copy the folder but do not persist annotations:
new_folder_instance = await Folder(id="syn123").copy(parent_id="syn456", copy_annotations=False)
| RAISES | DESCRIPTION |
|---|---|
ValueError
|
If the folder does not have an ID and parent_id to copy. |
Source code in synapseclient/models/protocols/folder_protocol.py
93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 | |
sync_from_synapse(path: Optional[str] = None, recursive: bool = True, download_file: bool = True, if_collision: str = COLLISION_OVERWRITE_LOCAL, failure_strategy: FailureStrategy = LOG_EXCEPTION, *, synapse_client: Optional[Synapse] = None) -> Self
Sync this container and all possible sub-folders from Synapse. By default this
will download the files that are found and it will populate the
files and folders attributes with the found files and folders. If you only
want to retrieve the full tree of metadata about your container specify
download_file as False.
This works similar to synapseutils.syncFromSynapse, however, this does not currently support the writing of data to a manifest TSV file. This will be a future enhancement.
Only Files and Folders are supported at this time to be synced from synapse.
| PARAMETER | DESCRIPTION |
|---|---|
path
|
An optional path where the file hierarchy will be reproduced. If not specified the files will by default be placed in the synapseCache. |
recursive
|
Whether or not to recursively get the entire hierarchy of the folder and sub-folders.
TYPE:
|
download_file
|
Whether to download the files found or not.
TYPE:
|
if_collision
|
Determines how to handle file collisions. May be
TYPE:
|
failure_strategy
|
Determines how to handle failures when retrieving children under this Folder and an exception occurs.
TYPE:
|
synapse_client
|
If not passed in and caching was not disabled by
|
| RETURNS | DESCRIPTION |
|---|---|
Self
|
The object that was called on. This will be the same object that was called on to start the sync. |
Using this function
Suppose I want to walk the immediate children of a folder without downloading the files:
from synapseclient import Synapse
from synapseclient.models import Folder
syn = Synapse()
syn.login()
my_folder = Folder(id="syn12345")
my_folder.sync_from_synapse(download_file=False, recursive=False)
for folder in my_folder.folders:
print(folder.name)
for file in my_folder.files:
print(file.name)
Suppose I want to download the immediate children of a folder:
from synapseclient import Synapse
from synapseclient.models import Folder
syn = Synapse()
syn.login()
my_folder = Folder(id="syn12345")
my_folder.sync_from_synapse(path="/path/to/folder", recursive=False)
for folder in my_folder.folders:
print(folder.name)
for file in my_folder.files:
print(file.name)
Suppose I want to download the immediate all children of a Project and all sub-folders and files:
from synapseclient import Synapse
from synapseclient.models import Project
syn = Synapse()
syn.login()
my_project = Project(id="syn12345")
my_project.sync_from_synapse(path="/path/to/folder")
| RAISES | DESCRIPTION |
|---|---|
ValueError
|
If the folder does not have an id set. |
A sequence diagram for this method is as follows:
sequenceDiagram
autonumber
participant project_or_folder
activate project_or_folder
project_or_folder->>sync_from_synapse: Recursive search and download files
activate sync_from_synapse
opt Current instance not retrieved from Synapse
sync_from_synapse->>project_or_folder: Call `.get()` method
project_or_folder-->>sync_from_synapse: .
end
loop For each return of the generator
sync_from_synapse->>client: call `.getChildren()` method
client-->>sync_from_synapse: .
note over sync_from_synapse: Append to a running list
end
loop For each child
note over sync_from_synapse: Create all `pending_tasks` at current depth
alt Child is File
note over sync_from_synapse: Append `file.get()` method
else Child is Folder
note over sync_from_synapse: Append `folder.get()` method
alt Recursive is True
note over sync_from_synapse: Append `folder.sync_from_synapse()` method
end
end
end
loop For each task in pending_tasks
par `file.get()`
sync_from_synapse->>File: Retrieve File metadata and Optionally download
File->>client: `.get()`
client-->>File: .
File-->>sync_from_synapse: .
and `folder.get()`
sync_from_synapse->>Folder: Retrieve Folder metadataa
Folder->>client: `.get()`
client-->>Folder: .
Folder-->>sync_from_synapse: .
and `folder.sync_from_synapse()`
note over sync_from_synapse: This is a recursive call to `sync_from_synapse`
sync_from_synapse->>sync_from_synapse: Recursive call to `.sync_from_synapse()`
end
end
deactivate sync_from_synapse
deactivate project_or_folderSource code in synapseclient/models/protocols/storable_container_protocol.py
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get_permissions(*, synapse_client: Optional[Synapse] = None) -> Permissions
Get the permissions that the caller has on an Entity.
| PARAMETER | DESCRIPTION |
|---|---|
synapse_client
|
If not passed in and caching was not disabled by
|
| RETURNS | DESCRIPTION |
|---|---|
Permissions
|
A Permissions object |
Using this function:
Getting permissions for a Synapse Entity
permissions = File(id="syn123").get_permissions()
Getting access types list from the Permissions object
permissions.access_types
Source code in synapseclient/models/protocols/access_control_protocol.py
18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 | |
Get the ACL that a user or group has on an Entity.
| PARAMETER | DESCRIPTION |
|---|---|
principal_id
|
Identifier of a user or group (defaults to PUBLIC users)
TYPE:
|
synapse_client
|
If not passed in and caching was not disabled by
|
| RETURNS | DESCRIPTION |
|---|---|
List[str]
|
An array containing some combination of ['READ', 'UPDATE', 'CREATE', 'DELETE', 'DOWNLOAD', 'MODERATE', 'CHANGE_PERMISSIONS', 'CHANGE_SETTINGS'] or an empty array |
Source code in synapseclient/models/protocols/access_control_protocol.py
47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 | |
set_permissions(principal_id: int = None, access_type: List[str] = None, modify_benefactor: bool = False, warn_if_inherits: bool = True, overwrite: bool = True, *, synapse_client: Optional[Synapse] = None) -> Dict[str, Union[str, list]]
Sets permission that a user or group has on an Entity. An Entity may have its own ACL or inherit its ACL from a benefactor.
| PARAMETER | DESCRIPTION |
|---|---|
principal_id
|
Identifier of a user or group.
TYPE:
|
access_type
|
Type of permission to be granted. One or more of CREATE, READ, DOWNLOAD, UPDATE, DELETE, CHANGE_PERMISSIONS. Defaults to ['READ', 'DOWNLOAD'] |
modify_benefactor
|
Set as True when modifying a benefactor's ACL
TYPE:
|
warn_if_inherits
|
Set as False, when creating a new ACL. Trying to modify the ACL of an Entity that inherits its ACL will result in a warning
TYPE:
|
overwrite
|
By default this function overwrites existing permissions for the specified user. Set this flag to False to add new permissions non-destructively.
TYPE:
|
synapse_client
|
If not passed in and caching was not disabled by
|
| RETURNS | DESCRIPTION |
|---|---|
Dict[str, Union[str, list]]
|
An Access Control List object |
Setting permissions
Grant all registered users download access
File(id="syn123").set_permissions(principal_id=273948, access_type=['READ','DOWNLOAD'])
Grant the public view access
File(id="syn123").set_permissions(principal_id=273949, access_type=['READ'])
Source code in synapseclient/models/protocols/access_control_protocol.py
68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 | |
dataclass
¶
Bases: FileSynchronousProtocol, AccessControllable
A file within Synapse.
| ATTRIBUTE | DESCRIPTION |
|---|---|
id |
The unique immutable ID for this file. A new ID will be generated for new Files. Once issued, this ID is guaranteed to never change or be re-issued. |
name |
The name of this entity. Must be 256 characters or less. Names may only contain: letters, numbers, spaces, underscores, hyphens, periods, plus signs, apostrophes, and parentheses. If not specified, the name will be derived from the file name. |
path |
The path to the file on disk. Using shorthand This is used during a This is also used during a |
description |
The description of this file. Must be 1000 characters or less. |
parent_id |
The ID of the Entity that is the parent of this Entity. Setting this to a new value and storing it will move this File under the new parent. |
version_label |
The version label for this entity. Updates to the entity will increment the version number. |
version_comment |
The version comment for this entity |
data_file_handle_id |
ID of the file associated with this entity. You may define an existing data_file_handle_id to use the existing data_file_handle_id. The creator of the file must also be the owner of the data_file_handle_id to have permission to store the file. |
external_url |
The external URL of this file. If this is set AND |
activity |
The Activity model represents the main record of Provenance in Synapse. It is analygous to the Activity defined in the W3C Specification on Provenance. Activity cannot be removed during a store operation by setting it to None. You must use: synapseclient.models.Activity.delete_async or [synapseclient.models.Activity.disassociate_from_entity_async][]. |
annotations |
Additional metadata associated with the folder. The key is the name
of your desired annotations. The value is an object containing a list of
values (use empty list to represent no values for key) and the value type
associated with all values in the list. To remove all annotations set this
to an empty dict
TYPE:
|
| ATTRIBUTE | DESCRIPTION |
|---|---|
content_type |
(New Upload Only) Used to manually specify Content-type header, for example 'application/png' or 'application/json; charset=UTF-8'. If not specified, the content type will be derived from the file extension. This can be specified only during the initial store of this file or any time there is a new file to upload. In order to change this after the File has been created use synapseclient.models.File.change_metadata. |
content_size |
(New Upload Only)
The size of the file in bytes. This can be specified only during the initial
creation of the File. This is also only applicable to files not uploaded to
Synapse. ie: |
| ATTRIBUTE | DESCRIPTION |
|---|---|
content_md5 |
(Store only) The MD5 of the file is known. If not supplied this
will be computed in the client is possible. If supplied for a file entity
already stored in Synapse it will be calculated again to check if a new
upload needs to occur. This will not be filled in during a read for data. It
is only used during a store operation. To retrieve the md5 of the file after
read from synapse use the |
create_or_update |
(Store only)
Indicates whether the method should automatically perform an
update if the
TYPE:
|
force_version |
(Store only) Indicates whether the method should increment the version of the object if something within the entity has changed. For example updating the description or name. You may set this to False and an update to the entity will not increment the version. Updating the An update to the MD5 of the file will force a version update regardless of this flag.
TYPE:
|
is_restricted |
(Store only) If set to true, an email will be sent to the Synapse access control team to start the process of adding terms-of-use or review board approval for this entity. You will be contacted with regards to the specific data being restricted and the requirements of access. This may be used only by an administrator of the specified file.
TYPE:
|
merge_existing_annotations |
(Store only)
Works in conjunction with
TYPE:
|
associate_activity_to_new_version |
(Store only)
Works in conjunction with
TYPE:
|
synapse_store |
(Store only) Whether the File should be uploaded or if false: only the path should be stored when synapseclient.models.File.store is called.
TYPE:
|
| ATTRIBUTE | DESCRIPTION |
|---|---|
download_file |
(Get only) If True the file will be downloaded.
TYPE:
|
if_collision |
(Get only) Determines how to handle file collisions. Defaults to "keep.both". May be:
TYPE:
|
synapse_container_limit |
(Get only) A Synanpse ID used to limit the search in Synapse if file is specified as a local file. That is, if the file is stored in multiple locations in Synapse only the ones in the specified folder/project will be returned. |
| ATTRIBUTE | DESCRIPTION |
|---|---|
etag |
(Read Only) Synapse employs an Optimistic Concurrency Control (OCC) scheme to handle concurrent updates. Since the E-Tag changes every time an entity is updated it is used to detect when a client's current representation of an entity is out-of-date. |
created_on |
(Read Only) The date this entity was created. |
modified_on |
(Read Only) The date this entity was last modified. |
created_by |
(Read Only) The ID of the user that created this entity. |
modified_by |
(Read Only) The ID of the user that last modified this entity. |
version_number |
(Read Only) The version number issued to this version on the object. |
is_latest_version |
(Read Only) If this is the latest version of the object. |
file_handle |
(Read Only) The file handle associated with this entity.
TYPE:
|
Source code in synapseclient/models/file.py
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Functions¶
Get the file from Synapse. You may retrieve a File entity by either:
- id
- path
If you specify both, the id will take precedence.
If you specify the path and the file is stored in multiple locations in Synapse
only the first one found will be returned. The other matching files will be
printed to the console.
You may also specify a version_number to get a specific version of the file.
| PARAMETER | DESCRIPTION |
|---|---|
include_activity
|
If True the activity will be included in the file if it exists.
TYPE:
|
synapse_client
|
If not passed in and caching was not disabled by
|
| RETURNS | DESCRIPTION |
|---|---|
File
|
The file object. |
| RAISES | DESCRIPTION |
|---|---|
ValueError
|
If the file does not have an ID or path to get. |
Using this function
Assuming you have a file with the ID "syn123":
file_instance = File(id="syn123").get()
Assuming you want to download a file to this directory: "path/to/directory":
file_instance = File(path="path/to/directory").get()
Source code in synapseclient/models/protocols/file_protocol.py
117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 | |
store(parent: Optional[Union[Folder, Project]] = None, *, synapse_client: Optional[Synapse] = None) -> File
Store the file in Synapse. With this method you may:
- Upload a file into Synapse
- Update the metadata of a file in Synapse
- Store a File object in Synapse without updating a file by setting
synapse_storeto False. - Change the name of a file in Synapse by setting the
nameattribute of the File object. Also see the synapseclient.models.File.change_metadata method for changing the name of the downloaded file. - Moving a file to a new parent by setting the
parent_idattribute of the File object.
| PARAMETER | DESCRIPTION |
|---|---|
parent
|
The parent folder or project to store the file in. May also be
specified in the File object. If both are provided the parent passed
into |
synapse_client
|
If not passed in and caching was not disabled by
|
| RETURNS | DESCRIPTION |
|---|---|
File
|
The file object. |
Using this function
File with the ID syn123 at path path/to/file.txt:
file_instance = File(id="syn123", path="path/to/file.txt").store()
File at the path path/to/file.txt and a parent folder with the ID syn456:
file_instance = File(path="path/to/file.txt", parent_id="syn456").store()
File at the path path/to/file.txt and a parent folder with the ID syn456:
file_instance = File(path="path/to/file.txt").store(parent=Folder(id="syn456"))
Rename a file (Does not update the file on disk or the name of the downloaded file):
file_instance = File(id="syn123", download_file=False).get()
print(file_instance.name) ## prints, e.g., "my_file.txt"
file_instance.change_metadata(name="my_new_name_file.txt")
Rename a file, and the name of the file as downloaded (Does not update the file on disk):
file_instance = File(id="syn123", download_file=False).get()
print(file_instance.name) ## prints, e.g., "my_file.txt"
file_instance.change_metadata(name="my_new_name_file.txt", download_as="my_new_name_file.txt")
Source code in synapseclient/models/protocols/file_protocol.py
20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 | |
copy(parent_id: str, update_existing: bool = False, copy_annotations: bool = True, copy_activity: Union[str, None] = 'traceback', *, synapse_client: Optional[Synapse] = None) -> File
Copy the file to another Synapse location. Defaults to the latest version of the file, or the version_number specified in the instance.
| PARAMETER | DESCRIPTION |
|---|---|
parent_id
|
Synapse ID of a folder/project that the copied entity is being copied to
TYPE:
|
update_existing
|
When the destination has a file that has the same name, users can choose to update that file.
TYPE:
|
copy_annotations
|
True to copy the annotations.
TYPE:
|
copy_activity
|
Has three options to set the activity of the copied file: |
synapse_client
|
If not passed in and caching was not disabled by
|
| RETURNS | DESCRIPTION |
|---|---|
File
|
The copied file object. |
Using this function
Assuming you have a file with the ID "syn123" and you want to copy it to a folder with the ID "syn456":
new_file_instance = File(id="syn123").copy(parent_id="syn456")
Copy the file but do not persist annotations or activity:
new_file_instance = File(id="syn123").copy(parent_id="syn456", copy_annotations=False, copy_activity=None)
| RAISES | DESCRIPTION |
|---|---|
ValueError
|
If the file does not have an ID and parent_id to copy. |
Source code in synapseclient/models/protocols/file_protocol.py
254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 | |
Delete the file from Synapse.
| PARAMETER | DESCRIPTION |
|---|---|
version_only
|
If True only the version specified in the |
synapse_client
|
If not passed in and caching was not disabled by
|
| RETURNS | DESCRIPTION |
|---|---|
None
|
None |
| RAISES | DESCRIPTION |
|---|---|
ValueError
|
If the file does not have an ID to delete. |
ValueError
|
If the file does not have a version number to delete a version,
and |
Using this function
Assuming you have a file with the ID "syn123":
File(id="syn123").delete()
Source code in synapseclient/models/protocols/file_protocol.py
223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 | |
classmethod
¶
Wrapper for synapseclient.models.File.get.
| PARAMETER | DESCRIPTION |
|---|---|
synapse_id
|
The ID of the file in Synapse.
TYPE:
|
synapse_client
|
If not passed in and caching was not disabled by
|
| RETURNS | DESCRIPTION |
|---|---|
File
|
The file object. |
Using this function
Assuming you have a file with the ID "syn123":
file_instance = File.from_id(synapse_id="syn123")
Source code in synapseclient/models/protocols/file_protocol.py
164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 | |
classmethod
¶
Get the file from Synapse. If the path of the file matches multiple files within Synapse the first one found will be returned. The other matching files will be printed to the console.
Wrapper for synapseclient.models.File.get.
| PARAMETER | DESCRIPTION |
|---|---|
path
|
The path to the file on disk.
TYPE:
|
synapse_client
|
If not passed in and caching was not disabled by
|
| RETURNS | DESCRIPTION |
|---|---|
File
|
The file object. |
Using this function
Assuming you have a file at the path "path/to/file.txt":
file_instance = File.from_path(path="path/to/file.txt")
Source code in synapseclient/models/protocols/file_protocol.py
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change_metadata(name: Optional[str] = None, download_as: Optional[str] = None, content_type: Optional[str] = None, *, synapse_client: Optional[Synapse] = None) -> File
Change File Entity metadata for properties that are immutable after creation through the store method.
| PARAMETER | DESCRIPTION |
|---|---|
name
|
Specify to change the filename of a file as seen on Synapse. |
download_as
|
Specify filename to change the filename of a filehandle. |
content_type
|
Specify content type to change the content type of a filehandle. |
synapse_client
|
If not passed in and caching was not disabled by
|
| RETURNS | DESCRIPTION |
|---|---|
File
|
The file object. |
Using this function
Can be used to change the filename, the filename when the file is downloaded, or the file content-type without downloading:
file_entity = File(id="syn123", download_file=False).get()
print(os.path.basename(file_entity.path)) ## prints, e.g., "my_file.txt"
file_entity = file_entity.change_metadata(name="my_new_name_file.txt", download_as="my_new_downloadAs_name_file.txt", content_type="text/plain")
print(os.path.basename(file_entity.path)) ## prints, "my_new_downloadAs_name_file.txt"
print(file_entity.name) ## prints, "my_new_name_file.txt"
| RAISES | DESCRIPTION |
|---|---|
ValueError
|
If the file does not have an ID to change metadata. |
Source code in synapseclient/models/protocols/file_protocol.py
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get_permissions(*, synapse_client: Optional[Synapse] = None) -> Permissions
Get the permissions that the caller has on an Entity.
| PARAMETER | DESCRIPTION |
|---|---|
synapse_client
|
If not passed in and caching was not disabled by
|
| RETURNS | DESCRIPTION |
|---|---|
Permissions
|
A Permissions object |
Using this function:
Getting permissions for a Synapse Entity
permissions = File(id="syn123").get_permissions()
Getting access types list from the Permissions object
permissions.access_types
Source code in synapseclient/models/protocols/access_control_protocol.py
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Get the ACL that a user or group has on an Entity.
| PARAMETER | DESCRIPTION |
|---|---|
principal_id
|
Identifier of a user or group (defaults to PUBLIC users)
TYPE:
|
synapse_client
|
If not passed in and caching was not disabled by
|
| RETURNS | DESCRIPTION |
|---|---|
List[str]
|
An array containing some combination of ['READ', 'UPDATE', 'CREATE', 'DELETE', 'DOWNLOAD', 'MODERATE', 'CHANGE_PERMISSIONS', 'CHANGE_SETTINGS'] or an empty array |
Source code in synapseclient/models/protocols/access_control_protocol.py
47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 | |
set_permissions(principal_id: int = None, access_type: List[str] = None, modify_benefactor: bool = False, warn_if_inherits: bool = True, overwrite: bool = True, *, synapse_client: Optional[Synapse] = None) -> Dict[str, Union[str, list]]
Sets permission that a user or group has on an Entity. An Entity may have its own ACL or inherit its ACL from a benefactor.
| PARAMETER | DESCRIPTION |
|---|---|
principal_id
|
Identifier of a user or group.
TYPE:
|
access_type
|
Type of permission to be granted. One or more of CREATE, READ, DOWNLOAD, UPDATE, DELETE, CHANGE_PERMISSIONS. Defaults to ['READ', 'DOWNLOAD'] |
modify_benefactor
|
Set as True when modifying a benefactor's ACL
TYPE:
|
warn_if_inherits
|
Set as False, when creating a new ACL. Trying to modify the ACL of an Entity that inherits its ACL will result in a warning
TYPE:
|
overwrite
|
By default this function overwrites existing permissions for the specified user. Set this flag to False to add new permissions non-destructively.
TYPE:
|
synapse_client
|
If not passed in and caching was not disabled by
|
| RETURNS | DESCRIPTION |
|---|---|
Dict[str, Union[str, list]]
|
An Access Control List object |
Setting permissions
Grant all registered users download access
File(id="syn123").set_permissions(principal_id=273948, access_type=['READ','DOWNLOAD'])
Grant the public view access
File(id="syn123").set_permissions(principal_id=273949, access_type=['READ'])
Source code in synapseclient/models/protocols/access_control_protocol.py
68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 | |
dataclass
¶
A file handle is a pointer to a file stored in a specific location.
| ATTRIBUTE | DESCRIPTION |
|---|---|
id |
The ID of this FileHandle. All references to this FileHandle will use this ID. Synapse will generate this ID when the FileHandle is created. |
etag |
FileHandles are immutable from the perspective of the API. The only field that can be change is the previewId. When a new previewId is set, the etag will change. |
created_by |
The ID Of the user that created this file. |
created_on |
The date when this file was uploaded. |
modified_on |
The date when the file was modified. This is handled by the backend and cannot be modified. |
concrete_type |
This is used to indicate the implementation of this interface. For example, an S3FileHandle should be set to: org.sagebionetworks.repo.model.file.S3FileHandle |
content_type |
|
content_md5 |
The file's content MD5. |
file_name |
The short, user visible name for this file. |
storage_location_id |
The optional storage location descriptor. |
content_size |
The size of the file in bytes. |
status |
The status of the file handle as computed by the backend. This value cannot be changed, any file handle that is not AVAILABLE should not be used. |
bucket_name |
The name of the bucket where this file resides. |
key |
The path or resource name for this object. |
preview_id |
If this file has a preview, then this will be the file ID of the preview. |
is_preview |
Whether or not this is a preview of another file. |
external_url |
The URL of the file if it is stored externally. |
Source code in synapseclient/models/file.py
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dataclass
¶
Bases: TableSynchronousProtocol, AccessControllable
A Table represents the metadata of a table.
| ATTRIBUTE | DESCRIPTION |
|---|---|
id |
The unique immutable ID for this table. A new ID will be generated for new Tables. Once issued, this ID is guaranteed to never change or be re-issued |
name |
The name of this table. Must be 256 characters or less. Names may only contain: letters, numbers, spaces, underscores, hyphens, periods, plus signs, apostrophes, and parentheses |
parent_id |
The ID of the Entity that is the parent of this table. |
columns |
The columns of this table. |
description |
The description of this entity. Must be 1000 characters or less. |
etag |
Synapse employs an Optimistic Concurrency Control (OCC) scheme to handle concurrent updates. Since the E-Tag changes every time an entity is updated it is used to detect when a client's current representation of an entity is out-of-date. |
created_on |
The date this table was created. |
created_by |
The ID of the user that created this table. |
modified_on |
The date this table was last modified. In YYYY-MM-DD-Thh:mm:ss.sssZ format |
modified_by |
The ID of the user that last modified this table. |
version_number |
The version number issued to this version on the object. |
version_label |
The version label for this table |
version_comment |
The version comment for this table |
is_latest_version |
If this is the latest version of the object. |
is_search_enabled |
When creating or updating a table or view specifies if full text search should be enabled. Note that enabling full text search might slow down the indexing of the table or view. |
activity |
The Activity model represents the main record of Provenance in Synapse. It is analygous to the Activity defined in the W3C Specification on Provenance. Activity cannot be removed during a store operation by setting it to None. You must use: synapseclient.models.Activity.delete_async or [synapseclient.models.Activity.disassociate_from_entity_async][]. |
annotations |
Additional metadata associated with the table. The key is the name
of your desired annotations. The value is an object containing a list of
values (use empty list to represent no values for key) and the value type
associated with all values in the list. To remove all annotations set this
to an empty dict
TYPE:
|
Source code in synapseclient/models/table.py
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Functions¶
Get the metadata about the table from synapse.
| PARAMETER | DESCRIPTION |
|---|---|
synapse_client
|
If not passed in and caching was not disabled by
|
| RETURNS | DESCRIPTION |
|---|---|
Table
|
The Table instance stored in synapse. |
Source code in synapseclient/models/protocols/table_protocol.py
88 89 90 91 92 93 94 95 96 97 98 99 | |
Store non-row information about a table including the columns and annotations.
| PARAMETER | DESCRIPTION |
|---|---|
synapse_client
|
If not passed in and caching was not disabled by
|
| RETURNS | DESCRIPTION |
|---|---|
Table
|
The Table instance stored in synapse. |
Source code in synapseclient/models/protocols/table_protocol.py
75 76 77 78 79 80 81 82 83 84 85 86 | |
Takes in a path to a CSV and stores the rows to Synapse.
| PARAMETER | DESCRIPTION |
|---|---|
csv_path
|
The path to the CSV to store.
TYPE:
|
synapse_client
|
If not passed in and caching was not disabled by
|
| RETURNS | DESCRIPTION |
|---|---|
str
|
The path to the CSV that was stored. |
Source code in synapseclient/models/protocols/table_protocol.py
43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 | |
Delete rows from a table.
| PARAMETER | DESCRIPTION |
|---|---|
rows
|
The rows to delete.
TYPE:
|
synapse_client
|
If not passed in and caching was not disabled by
|
| RETURNS | DESCRIPTION |
|---|---|
None
|
None |
Source code in synapseclient/models/protocols/table_protocol.py
59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 | |
classmethod
¶
query(query: str, result_format: Union[CsvResultFormat, RowsetResultFormat] = None, *, synapse_client: Optional[Synapse] = None) -> Union[CsvFileTable, TableQueryResult, None]
Query for data on a table stored in Synapse.
| PARAMETER | DESCRIPTION |
|---|---|
query
|
The query to run.
TYPE:
|
result_format
|
The format of the results. Defaults to CsvResultFormat().
TYPE:
|
synapse_client
|
If not passed in and caching was not disabled by
|
| RETURNS | DESCRIPTION |
|---|---|
Union[CsvFileTable, TableQueryResult, None]
|
The results of the query. |
Source code in synapseclient/models/protocols/table_protocol.py
114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 | |
Delete the table from synapse.
| PARAMETER | DESCRIPTION |
|---|---|
synapse_client
|
If not passed in and caching was not disabled by
|
| RETURNS | DESCRIPTION |
|---|---|
None
|
None |
Source code in synapseclient/models/protocols/table_protocol.py
101 102 103 104 105 106 107 108 109 110 111 112 | |
get_permissions(*, synapse_client: Optional[Synapse] = None) -> Permissions
Get the permissions that the caller has on an Entity.
| PARAMETER | DESCRIPTION |
|---|---|
synapse_client
|
If not passed in and caching was not disabled by
|
| RETURNS | DESCRIPTION |
|---|---|
Permissions
|
A Permissions object |
Using this function:
Getting permissions for a Synapse Entity
permissions = File(id="syn123").get_permissions()
Getting access types list from the Permissions object
permissions.access_types
Source code in synapseclient/models/protocols/access_control_protocol.py
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Get the ACL that a user or group has on an Entity.
| PARAMETER | DESCRIPTION |
|---|---|
principal_id
|
Identifier of a user or group (defaults to PUBLIC users)
TYPE:
|
synapse_client
|
If not passed in and caching was not disabled by
|
| RETURNS | DESCRIPTION |
|---|---|
List[str]
|
An array containing some combination of ['READ', 'UPDATE', 'CREATE', 'DELETE', 'DOWNLOAD', 'MODERATE', 'CHANGE_PERMISSIONS', 'CHANGE_SETTINGS'] or an empty array |
Source code in synapseclient/models/protocols/access_control_protocol.py
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set_permissions(principal_id: int = None, access_type: List[str] = None, modify_benefactor: bool = False, warn_if_inherits: bool = True, overwrite: bool = True, *, synapse_client: Optional[Synapse] = None) -> Dict[str, Union[str, list]]
Sets permission that a user or group has on an Entity. An Entity may have its own ACL or inherit its ACL from a benefactor.
| PARAMETER | DESCRIPTION |
|---|---|
principal_id
|
Identifier of a user or group.
TYPE:
|
access_type
|
Type of permission to be granted. One or more of CREATE, READ, DOWNLOAD, UPDATE, DELETE, CHANGE_PERMISSIONS. Defaults to ['READ', 'DOWNLOAD'] |
modify_benefactor
|
Set as True when modifying a benefactor's ACL
TYPE:
|
warn_if_inherits
|
Set as False, when creating a new ACL. Trying to modify the ACL of an Entity that inherits its ACL will result in a warning
TYPE:
|
overwrite
|
By default this function overwrites existing permissions for the specified user. Set this flag to False to add new permissions non-destructively.
TYPE:
|
synapse_client
|
If not passed in and caching was not disabled by
|
| RETURNS | DESCRIPTION |
|---|---|
Dict[str, Union[str, list]]
|
An Access Control List object |
Setting permissions
Grant all registered users download access
File(id="syn123").set_permissions(principal_id=273948, access_type=['READ','DOWNLOAD'])
Grant the public view access
File(id="syn123").set_permissions(principal_id=273949, access_type=['READ'])
Source code in synapseclient/models/protocols/access_control_protocol.py
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dataclass
¶
Bases: ActivitySynchronousProtocol
An activity is a Synapse object that helps to keep track of what objects were used
in an analysis step, as well as what objects were generated. Thus, all relationships
between Synapse objects and an activity are governed by dependencies. That is, an
activity needs to know what it used, and outputs need to know what activity
they were generatedBy.
| ATTRIBUTE | DESCRIPTION |
|---|---|
id |
The unique immutable ID for this actvity. |
name |
A name for this Activity. |
description |
A description for this Activity. |
etag |
Synapse employs an Optimistic Concurrency Control (OCC) scheme to handle concurrent updates. Since the E-Tag changes every time an entity is updated it is used to detect when a client's current representation of an entity is out-of-date. |
created_on |
The date this object was created. |
modified_on |
The date this object was last modified. |
created_by |
The user that created this object. |
modified_by |
The user that last modified this object. |
used |
The entities or URLs used by this Activity.
TYPE:
|
executed |
The entities or URLs executed by this Activity.
TYPE:
|
Source code in synapseclient/models/activity.py
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dataclass
¶
Reference to a Synapse entity that was used or executed by an Activity.
| ATTRIBUTE | DESCRIPTION |
|---|---|
target_id |
The ID of the entity to which this reference refers. |
target_version_number |
The version number of the entity to which this reference refers. |
Source code in synapseclient/models/activity.py
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dataclass
¶
URL that was used or executed by an Activity such as a link to a GitHub commit or a link to a specific version of a software tool.
| ATTRIBUTE | DESCRIPTION |
|---|---|
name |
The name of the URL. |
url |
The external URL of the file that was used such as a link to a GitHub commit or a link to a specific version of a software tool. |
Source code in synapseclient/models/activity.py
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dataclass
¶
Bases: TeamSynchronousProtocol
Represents a Synapse Team. User definable fields are:
| ATTRIBUTE | DESCRIPTION |
|---|---|
id |
The ID of the team |
name |
The name of the team |
description |
A short description of the team |
icon |
A file handle ID for the icon image of the team |
can_public_join |
True if members can join without an invitation or approval |
can_request_membership |
True if users can create a membership request to join |
etag |
Synapse employs an Optimistic Concurrency Control (OCC) scheme to handle concurrent updates Since the E-Tag changes every time an entity is updated it is used to detect when a client's current representation of an entity is out-of-date. |
created_on |
The date this team was created |
modified_on |
The date this team was last modified |
created_by |
The ID of the user that created this team |
modified_by |
The ID of the user that last modified this team |
Source code in synapseclient/models/team.py
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dataclass
¶
Bases: UserProfileSynchronousProtocol
UserProfile represents a user's profile in the system.
| ATTRIBUTE | DESCRIPTION |
|---|---|
id |
A foreign key to the ID of the 'principal' object for the user. |
etag |
Synapse employs an Optimistic Concurrency Control (OCC) scheme to handle concurrent updates. Since the E-Tag changes every time an entity is updated it is used to detect when a client's currentrepresentation of an entity is out-of-date. |
first_name |
This person's given name (forename) |
last_name |
This person's family name (surname) |
emails |
The list of user email addresses registered to this user. |
open_ids |
The list of OpenIds bound to this user's account. |
username |
A name chosen by the user that uniquely identifies them. |
display_name |
This field is deprecated and will always be null. |
r_studio_url |
URL for RStudio server assigned to the user. |
summary |
A summary description about this person. |
position |
This person's current position title. |
location |
This person's location. |
industry |
The industry/discipline that this person is associated with. |
company |
This person's current affiliation. |
profile_picure_file_handle_id |
The File Handle id of the user's profile picture. |
url |
A link to more information about this person. |
team_name |
This person's default team name. |
notification_settings |
Contains a user's notification settings. |
preferences |
User preferences
TYPE:
|
created_on |
The date this profile was created. |
Source code in synapseclient/models/user.py
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dataclass
¶
A UserPreference represents a user preference in the system.
| ATTRIBUTE | DESCRIPTION |
|---|---|
name |
The name of the user preference. |
value |
The value of the user preference. |
Source code in synapseclient/models/user.py
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dataclass
¶
Bases: AnnotationsSynchronousProtocol
Annotations that can be applied to a number of Synapse resources to provide additional information.
| ATTRIBUTE | DESCRIPTION |
|---|---|
annotations |
Additional metadata associated with the object. The key is the name of your desired annotations. The value is an object containing a list of string values (use empty list to represent no values for key) and the value type associated with all values in the list.
TYPE:
|
id |
ID of the object to which this annotation belongs. Not required if being used as a member variable on another class. |
etag |
Etag of the object to which this annotation belongs. This field must match the current etag on the object. Not required if being used as a member variable on another class. |
Source code in synapseclient/models/annotations.py
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Functions¶
classmethod
¶
from_dict(synapse_annotations: dict) -> Union[Dict[str, Union[List[str], List[bool], List[float], List[int], List[date], List[datetime]]], None]
Convert the annotations from the format the synapse rest API works in - to the format used by this class.
| PARAMETER | DESCRIPTION |
|---|---|
synapse_annotations
|
The annotations from the synapse rest API.
TYPE:
|
| RETURNS | DESCRIPTION |
|---|---|
Union[Dict[str, Union[List[str], List[bool], List[float], List[int], List[date], List[datetime]]], None]
|
The annotations in python class format or None. |
Source code in synapseclient/models/annotations.py
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Bases: AccessControllableSynchronousProtocol
Mixin for objects that can be controlled by an Access Control List (ACL).
In order to use this mixin, the class must have an id attribute.
Source code in synapseclient/models/mixins/access_control.py
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Attributes¶
class-attribute
instance-attribute
¶
The unique immutable ID for this entity. A new ID will be generated for new Files. Once issued, this ID is guaranteed to never change or be re-issued.
Functions¶
async
¶
get_permissions_async(*, synapse_client: Optional[Synapse] = None) -> Permissions
Get the permissions that the caller has on an Entity.
| PARAMETER | DESCRIPTION |
|---|---|
synapse_client
|
If not passed in and caching was not disabled by
|
| RETURNS | DESCRIPTION |
|---|---|
Permissions
|
A Permissions object |
Using this function:
Getting permissions for a Synapse Entity
permissions = await File(id="syn123").get_permissions_async()
Getting access types list from the Permissions object
permissions.access_types
Source code in synapseclient/models/mixins/access_control.py
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async
¶
Get the ACL that a user or group has on an Entity.
| PARAMETER | DESCRIPTION |
|---|---|
principal_id
|
Identifier of a user or group (defaults to PUBLIC users)
TYPE:
|
synapse_client
|
If not passed in and caching was not disabled by
|
| RETURNS | DESCRIPTION |
|---|---|
List[str]
|
An array containing some combination of ['READ', 'UPDATE', 'CREATE', 'DELETE', 'DOWNLOAD', 'MODERATE', 'CHANGE_PERMISSIONS', 'CHANGE_SETTINGS'] or an empty array |
Source code in synapseclient/models/mixins/access_control.py
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async
¶
set_permissions_async(principal_id: int = None, access_type: List[str] = None, modify_benefactor: bool = False, warn_if_inherits: bool = True, overwrite: bool = True, *, synapse_client: Optional[Synapse] = None) -> Dict[str, Union[str, list]]
Sets permission that a user or group has on an Entity. An Entity may have its own ACL or inherit its ACL from a benefactor.
| PARAMETER | DESCRIPTION |
|---|---|
principal_id
|
Identifier of a user or group.
TYPE:
|
access_type
|
Type of permission to be granted. One or more of CREATE, READ, DOWNLOAD, UPDATE, DELETE, CHANGE_PERMISSIONS. Defaults to ['READ', 'DOWNLOAD'] |
modify_benefactor
|
Set as True when modifying a benefactor's ACL
TYPE:
|
warn_if_inherits
|
Set as False, when creating a new ACL. Trying to modify the ACL of an Entity that inherits its ACL will result in a warning
TYPE:
|
overwrite
|
By default this function overwrites existing permissions for the specified user. Set this flag to False to add new permissions non-destructively.
TYPE:
|
synapse_client
|
If not passed in and caching was not disabled by
|
| RETURNS | DESCRIPTION |
|---|---|
Dict[str, Union[str, list]]
|
An Access Control List object |
Setting permissions
Grant all registered users download access
await File(id="syn123").set_permissions_async(principal_id=273948, access_type=['READ','DOWNLOAD'])
Grant the public view access
await File(id="syn123").set_permissions_async(principal_id=273949, access_type=['READ'])
Source code in synapseclient/models/mixins/access_control.py
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Bases: StorableContainerSynchronousProtocol
Mixin for objects that can have Folders and Files stored in them.
In order to use this mixin, the class must have the following attributes:
idfilesfolders_last_persistent_instance
The class must have the following method:
get
Source code in synapseclient/models/mixins/storable_container.py
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Functions¶
async
¶
Used to satisfy the usage in this mixin from the parent class.
Source code in synapseclient/models/mixins/storable_container.py
55 56 | |
async
¶
sync_from_synapse_async(path: Optional[str] = None, recursive: bool = True, download_file: bool = True, if_collision: str = COLLISION_OVERWRITE_LOCAL, failure_strategy: FailureStrategy = LOG_EXCEPTION, include_activity: bool = True, follow_link: bool = False, link_hops: int = 1, queue: Queue = None, *, synapse_client: Optional[Synapse] = None) -> Self
Sync this container and all possible sub-folders from Synapse. By default this
will download the files that are found and it will populate the
files and folders attributes with the found files and folders. If you only
want to retrieve the full tree of metadata about your container specify
download_file as False.
This works similar to synapseutils.syncFromSynapse, however, this does not currently support the writing of data to a manifest TSV file. This will be a future enhancement.
Only Files and Folders are supported at this time to be synced from synapse.
| PARAMETER | DESCRIPTION |
|---|---|
path
|
An optional path where the file hierarchy will be reproduced. If not specified the files will by default be placed in the synapseCache. |
recursive
|
Whether or not to recursively get the entire hierarchy of the folder and sub-folders.
TYPE:
|
download_file
|
Whether to download the files found or not.
TYPE:
|
if_collision
|
Determines how to handle file collisions. May be
TYPE:
|
failure_strategy
|
Determines how to handle failures when retrieving children under this Folder and an exception occurs.
TYPE:
|
include_activity
|
Whether to include the activity of the files.
TYPE:
|
follow_link
|
Whether to follow a link entity or not. Links can be used to point at other Synapse entities.
TYPE:
|
link_hops
|
The number of hops to follow the link. A number of 1 is used to prevent circular references. There is nothing in place to prevent infinite loops. Be careful if setting this above 1.
TYPE:
|
queue
|
An optional queue to use to download files in parallel.
TYPE:
|
synapse_client
|
If not passed in and caching was not disabled by
|
| RETURNS | DESCRIPTION |
|---|---|
Self
|
The object that was called on. This will be the same object that was called on to start the sync. |
Using this function
Suppose I want to walk the immediate children of a folder without downloading the files:
from synapseclient import Synapse
from synapseclient.models import Folder
syn = Synapse()
syn.login()
my_folder = Folder(id="syn12345")
await my_folder.sync_from_synapse_async(download_file=False, recursive=False)
for folder in my_folder.folders:
print(folder.name)
for file in my_folder.files:
print(file.name)
Suppose I want to download the immediate children of a folder:
from synapseclient import Synapse
from synapseclient.models import Folder
syn = Synapse()
syn.login()
my_folder = Folder(id="syn12345")
await my_folder.sync_from_synapse_async(path="/path/to/folder", recursive=False)
for folder in my_folder.folders:
print(folder.name)
for file in my_folder.files:
print(file.name)
Suppose I want to download the immediate all children of a Project and all sub-folders and files:
from synapseclient import Synapse
from synapseclient.models import Project
syn = Synapse()
syn.login()
my_project = Project(id="syn12345")
await my_project.sync_from_synapse_async(path="/path/to/folder")
| RAISES | DESCRIPTION |
|---|---|
ValueError
|
If the folder does not have an id set. |
A sequence diagram for this method is as follows:
sequenceDiagram
autonumber
participant project_or_folder
activate project_or_folder
project_or_folder->>sync_from_synapse: Recursive search and download files
activate sync_from_synapse
opt Current instance not retrieved from Synapse
sync_from_synapse->>project_or_folder: Call `.get()` method
project_or_folder-->>sync_from_synapse: .
end
loop For each return of the generator
sync_from_synapse->>client: call `.getChildren()` method
client-->>sync_from_synapse: .
note over sync_from_synapse: Append to a running list
end
loop For each child
note over sync_from_synapse: Create all `pending_tasks` at current depth
alt Child is File
note over sync_from_synapse: Append `file.get()` method
else Child is Folder
note over sync_from_synapse: Append `folder.get()` method
alt Recursive is True
note over sync_from_synapse: Append `folder.sync_from_synapse()` method
end
else Child is Link and hops > 0
note over sync_from_synapse: Append task to follow link
end
end
loop For each task in pending_tasks
par `file.get()`
sync_from_synapse->>File: Retrieve File metadata and Optionally download
File->>client: `.get()`
client-->>File: .
File-->>sync_from_synapse: .
and `folder.get()`
sync_from_synapse->>Folder: Retrieve Folder metadataa
Folder->>client: `.get()`
client-->>Folder: .
Folder-->>sync_from_synapse: .
and `folder.sync_from_synapse_async()`
note over sync_from_synapse: This is a recursive call to `sync_from_synapse`
sync_from_synapse->>sync_from_synapse: Recursive call to `.sync_from_synapse_async()`
and `_follow_link`
sync_from_synapse ->>client: call `get_entity_id_bundle2` function
client-->sync_from_synapse: .
note over sync_from_synapse: Do nothing if not link
note over sync_from_synapse: call `_create_task_for_child` and execute
end
end
deactivate sync_from_synapse
deactivate project_or_folderSource code in synapseclient/models/mixins/storable_container.py
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Recursively loop over all of the already retrieved files and folders and return a list of all files in the container.
| RETURNS | DESCRIPTION |
|---|---|
List[File]
|
A list of all files in the container. |
Source code in synapseclient/models/mixins/storable_container.py
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Recursively loop over all of the already retrieved files and folders. Then return back a dictionary where the key is the path to the directory at each level. The value is a list of all files in that directory AND all files in the child directories.
This is used during the creation of the manifest TSV file during the syncFromSynapse utility function.
Using this function
Returning back a dict with 2 keys:
Given:
root_folder
├── sub_folder
│ ├── file1.txt
│ └── file2.txt
Returns:
{
"root_folder": [file1, file2],
"root_folder/sub_folder": [file1, file2]
}
Returning back a dict with 3 keys:
Given:
root_folder
├── sub_folder_1
│ ├── file1.txt
├── sub_folder_2
│ └── file2.txt
Returns:
{
"root_folder": [file1, file2],
"root_folder/sub_folder_1": [file1]
"root_folder/sub_folder_2": [file2]
}
| PARAMETER | DESCRIPTION |
|---|---|
root_path
|
The root path where the top level files are stored.
TYPE:
|
| RETURNS | DESCRIPTION |
|---|---|
Dict[str, List[File]]
|
A dictionary where the key is the path to the directory at each level. The value is a list of all files in that directory AND all files in the child directories. |
Source code in synapseclient/models/mixins/storable_container.py
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Bases: Enum
When storing a large number of items through bulk actions like
Project(id="syn123").store() or Folder(id="syn456").store() individual failures
may occur. Passing this ENUM will allow you to define how you want to respond to
failures.
Source code in synapseclient/models/services/storable_entity_components.py
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Attributes¶
class-attribute
instance-attribute
¶
RAISE_EXCEPTION = 'RAISE_EXCEPTION'
An exception is raised on the first failure and all tasks yet to be completed are cancelled. The exception will also be logged.
class-attribute
instance-attribute
¶
LOG_EXCEPTION = 'LOG_EXCEPTION'
An exception is logged and all tasks yet to be completed continue to be processed.