Downloading Data Programmatically
- Stacey Taylor (Unlicensed)
- Jessica Vera
- alex.knoll (Unlicensed)
- Bryan Fauble
Data in Synapse can be downloaded using our programmatic clients (Python, R, and command line), or from the Synapse UI. In this guide, you will learn the basic commands to download data programmatically.
Downloading Files
Before you begin, it is important to understand that most items in Synapse have a unique identifier associated with them. This identifier is called a Synapse ID, or a synID. The synID format is the prefix “syn” followed by 8 numbers (for example, syn12345678). Items that have unique synIDs in Synapse are: files, folders, projects, tables, views, wikis, links, and Docker repositories. You can use synIDs to refer to specific items when working with Synapse programmatically.
When using the Python, R, or command line clients, files can be downloaded by using the get command. Downloaded files are stored and/or registered in a cache. By default, the cache location is in your home directory in a hidden folder named .synapseCache. Whenever the get function is invoked, the cache is checked to see if the same file is already present by checking its MD5 checksum. If it already exists, the file will not be downloaded again. In other words, if the current version of a file has already been downloaded, Synapse will not re-download the same file.
For the Python and R clients, the default download location is the Synapse cache. The command line client downloads to your current working directory. On the web, your own browser settings determine the download location for files. The Synapse cache is not updated to reflect downloads through a web browser. In all cases you can specify the directory in which to download the file.
For example, to download the experimental protocol on Adult Mouse Cardiac Myocyte Isolation (syn315811) from the Progenitor Cell Biology Consortium (PCBC) you would run the following:
Command line
synapse get syn3158111
Python
import synapseclient
syn = synapseclient.Synapse()
syn.login()
entity = syn.get("syn3158111")
R
library(synapser)
synLogin()
entity <- synGet("syn3158111")
Once a file has been downloaded, you can find the file path using the following:
Command line
Python
R
Downloading a Specific File Version
If there are multiple versions of a file, a specific version can be downloaded by passing the version parameter.
In this example, there are multiple versions of an miRNA FASTQ file (syn3260973) from the Progenitor Cell Biology Consortium. To download the first version:
Command line
Python
R
See Versioning for more details.
Downloading Linked Data
When you click on a link on the Synapse website, it will redirect you to the linked entity. The followLink parameter will have to be specified when using the programmatic clients or you will only retrieve the link itself without downloading the linked entity.
Command line
Python
R
Downloading Location
To override the default download location, you can specify the downloadLocation parameter.
Command line
Python
R
Finding and Downloading Files via Annotations
Files can be annotated in Synapse to help organize your data and make files findable. In order to search the annotations, you must create a file view first.
For example, the PCBC Project has a table listing sequencing data files that are annotated. To find all mRNA fastq files originating from CD34+ cells in the we can query by:
Command line
Python
R
Once you’ve queried for the files of interest, they can be downloaded using the following:
Command line
Python
R
Recursive Downloading
The folder structure that is present on Synapse can be maintained by recursive downloading.
Command line
Python
R
Downloading Wikis
The structure of a wiki page can be extracted through the R and Python clients. The ID, title, and parent wiki page of each sub-wiki page is also determined through the same method.
Python
R
The Markdown content within a wiki page can be downloaded if you know the synID and page ID for the wiki. The wiki page ID can either be obtained through the above method or can be found in the URL. For example, in the URL www.synapse.org/#!Synapse:syn00123/wiki/123456, the last 6 digits of the URL path is the wiki page ID (123456).
Python
R
Downloading in Bulk
Files can be downloaded in bulk using the syncFromSynapse function found in the synapseutils helper package. This function crawls all the subfolders of the project or folder that you specify and retrieves all the files that have not been downloaded. By default, the files will be downloaded into your synapseCache, but a different download location can be specified with the path parameter. If you do download to a location out side of synapseCache, this function will also create a tab-delimited manifest of all the files along with their metadata (path, provenance, annotations, etc).
Python
R