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. syn00123).
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 File.
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.
For example, to get the experimental protocol file on Adult Mouse Cardiac Myocyte Isolation (syn3158111) from the Progenitor Cell Biology Consortium (PCBC) you would run the following:
synapse get syn3158111
import synapseclient
syn = synapseclient.Synapse()
syn.login()
entity = syn.get("syn3158111")
library(synapser)
synLogin()
entity <- synGet("syn3158111")
Once a File has been downloaded, you can find the filepath using the following:
# When downloading using the command line client, it will print the filepath of where the file was saved to.
filepath = entity.path
filepath <- entity$path
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:
synapse get syn3260973 -v 1
entity = syn.get("syn3260973", version=1)
entity <- synGet("syn3260973", version=1)
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.
synapse get syn1234 --followLink
import synapseclient
syn = synapseclient.login()
linkEnt = syn.get("syn1234")
entity = syn.get("syn1234", followLink=True)
library(synapser)
synLogin()
linkEnt = synGet("syn1234")
entity = synGet("syn1234", followLink=TRUE)
To override the default download location (to not download to the Synapse cache directory, for example), you can specify the downloadLocation parameter.
synapse get syn00123 --downloadLocation /path/to/folder
entity = syn.get("syn00123", downloadLocation="/path/to/folder")
entity <- synGet("syn00123", downloadLocation="/path/to/folder")
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.
For example, the PCBC Project has a table listing sequencing data files that have been annotated. To find all mRNA fastq files originating from CD34+ cells in the we can query by:
synapse query 'select * from syn7511263 where dataType="mRNA" AND fileType="fastq" AND Cell_Type_of_Origin="CD34+ cells"'
results = syn.tableQuery('select * from syn7511263 where dataType="mRNA" AND fileType="fastq" AND Cell_Type_of_Origin="CD34+ cells"')
results <- synTableQuery('select * from syn7511263 where dataType="mRNA" AND fileType="fastq" AND Cell_Type_of_Origin="CD34+ cells"')
df <- as.data.frame(results)
Once you’ve queried for the files of interest, they can be downloaded using the following:
synapse get -q 'select * from syn7511263 where dataType="mRNA" AND fileType="fastq" AND Cell_Type_of_Origin="CD34+ cells"'
results = syn.tableQuery('select * from syn7511263 where dataType="mRNA" AND fileType="fastq" AND Cell_Type_of_Origin="CD34+ cells"')
entity = [syn.get(r['file.id']) for r in results]
results <- synTableQuery('select * from syn7511263 where dataType="mRNA" AND fileType="fastq" AND Cell_Type_of_Origin="CD34+ cells"')
df <- as.data.frame(results)
entity <- lapply(df$file.id, function(x) synGet(x))
The folder structure that is present on Synapse can be maintained by recursive downloading.
synapse get -r syn2390898
import synapseutils
import synapseclient
syn = synapseclient.login()
files = synapseutils.syncFromSynapse(syn, 'syn2390898')
# Unfortunately, this feature is not currently available in the R client
Please view here to learn how to use Tables.
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.
wiki = syn.getWikiHeaders("syn00123")
entity <- synGet("syn00123")
wiki <- synGetWikiHeaders(entity)
The Markdown and other information of a Project sub-Wiki page can be obtained by knowing the id of the Wiki. 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.
wiki = syn.getWiki("syn00123", 12345)
entity <- synGet("syn00123")
wiki <- synGetWiki(entity, 12345)
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).
# Load required libraries
import synapseclient
import synapseutils
# login to Synapse
syn = synapseclient.login(email='me@example.com', password='secret', rememberMe=True)
# download all the files in folder syn123 to a local folder called "myFolder"
all_files = synapseutils.syncFromSynapse(syn, entity='syn123', path='/path/to/myFolder')
# Load required libraries
library(synapser)
library(synapserutils)
# login to Synapse
synLogin(email='me@example.com', password='secret', rememberMe=TRUE)
# download all the files in folder syn123 to a local folder called "myFolder"
all_files = syncFromSynapse(entity='syn123', path='/path/to/myFolder')
Versioning, Tables, Wikis, File Views, Annotations and Queries
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Let us know what was unclear or what has not been covered. Reader feedback is key to making the documentation better, so please let us know or open an issue in our Github repository (Sage-Bionetworks/synapseDocs).