Provides tools for monitoring modified Synapse entities.
pip install synapsemonitor
usage: synapsemonitor [-h] [-c file] [--log {debug,info,warning,error}] {monitor,create} ...
Checks for new or modified Synapse entities. If a Project or Folder entity is specified, all File entity
descendants will be monitored. Users can create a Synapse File View to track the contents of Projects or
Folders with many file entities more efficiently. You can use the `create` function provided in this package
to create a File View.
optional arguments:
-h, --help show this help message and exit
-c file, --synapse_config file
Synapse config file with user credentials: (default
/Users/hhunterzinck/.synapseConfig)
--log {debug,info,warning,error}, -l {debug,info,warning,error}
Set logging output level (default: error)
commands:
The following commands are available:
{monitor,create} For additional help: "synapsemonitor <COMMAND> -h"
monitor Find new or modified File entities.
create Creates a File View that will list all the File entities under the specified scopes
(Synapse Folders or Projects). This will allow you to query for the files contained in
your specified scopes. This will NOT track the other entities currently: PROJECT,
TABLE, FOLDER, VIEW, DOCKER.
Monitors Synapse entities for modifications and sends an email through the Synapse messaging system to the user specified when modified entities are detected. Prints a list of modified File entities. If the specified entity is a container (Project or Folder), all descendant File entities are monitored. If the specified entity is a File View, all contained enties are monitored.
usage: synapsemonitor monitor [-h] [--users USERS [USERS ...]] [--output OUTPUT] [--email_subject EMAIL_SUBJECT] [--rate rate] synapse_id
positional arguments:
synapse_id Synapse ID of entity to be monitored.
optional arguments:
-h, --help show this help message and exit
--users USERS [USERS ...], -u USERS [USERS ...]
User Id or username of individuals to send report. If not specified, defaults to logged in Synapse user.
--output OUTPUT, -o OUTPUT
Output modified entities into this csv file. (default: None)
--email_subject EMAIL_SUBJECT, -e EMAIL_SUBJECT
Sets the subject heading of the email sent out. (default: New Synapse Files)
--value value, -v value
Find modifications to File entities in the last
{value} {unit}. (default: 1)
--unit unit, -t unit Find modifications to File entities in the last
{value} {unit}. (default: 'day')
Creates a File View that will list all the File entities under the specified scopes (Synapse Folders or Projects). This will allow you to query for the files contained in your specified scopes. This will NOT track the other entities currently: PROJECT, TABLE, FOLDER, VIEW, DOCKER.
usage: synapsemonitor create [-h] --scope_ids SCOPE_IDS [SCOPE_IDS ...] NAME project_id
positional arguments:
NAME File View name
project_id Synapse Project Id to store file view in
optional arguments:
-h, --help show this help message and exit
--scope_ids SCOPE_IDS [SCOPE_IDS ...]
Synapse Folder / Project Ids
There is a Docker repository that is automatically build: sagebionetworks/synapsemonitor. See the available tags here. It is always recommended to use a tag other than latest because the latest tag can change. This package requires authentication to Synapse and we highly recommend using a Synapse PAT. For more information on the PAT.
docker run -e SYNAPSE_AUTH_TOKEN={your_auth_token_here} sagebionetworks/synapsemonitor:v0.0.2 -h
Often times you will want to run this code periodically to continuously track changes. One way you can do this is to set up a cronjob. Follow this beginners guide. Note: you will most likely want to create an ec2 to run your cronjob instead of your laptop.
There are also other technologies that support scheduled execution of code such as AWS lambdas, AWS batch, Kubernetes and etc. The above is a way of setting a cronjob on your laptop or ec2.