Data in Synapse can be downloaded using the programmatic clients (Python, R, and command line) as well as the web client.
Every entity in Synapse has a unique synID associated with it. It can be found on every entity page next to
Synapse ID:, starting with
syn ending with numbers (i.e.
Files can be downloaded by using the
get command. By default, the
File downloaded will always be the most recent version. If the current version of the
File has already been downloaded, it will not re-download the
When using the Python, R, or command line clients, files downloaded using the
get command 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.
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.
File has been downloaded, you can find the filepath using the following:
If there are multiple versions of a
File, a specific version can be downloaded by passing the
In this example, there are multiple versions of an miRNA FASTQ file (syn3260973) from the Progenitor Cell Biology Consortium. To download the first version:
See versioning for more details.
When you click on a Link entity 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.
To override the default download location (to not download to the Synapse cache directory, for example), you can specify the
Files can be annotated to facilitate finding them. In order to search the annotations, a File View must be created first. It is possible to query based on any of the annotations attached to the files.
Once you’ve queried for the files of interest, they can be downloaded using the following:
The folder structure that is present on Synapse can be maintained by recursive downloading.
Please view here to learn how to use
The structure of a project’s
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.
The Markdown and other information of a
Wiki page can be obtained by knowing the id of the
Wiki page id can either be obtained through the above method or can be found in the URL “www.synapse.org/#!Synapse:syn00123/wiki/12345” where 12345 is the
Wiki page id.
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/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).