Is there a way to bulk download all the tables? Clicking on individual links to download diverse data for 34K individuals is not feasible.
Created by Naisha Shah nshah Here is a resource describing system dependencies that may need to be configured: https://r-docs.synapse.org/articles/systemDependencies.html
Also, information about what command you ran to get the above error would be helpful to understand why you are seeing such an error.
Hope this is helpful. Also which r version synapse works on? I tried with R `3.3.0,3.4.3,3.5.0,3.6.0.` Can I know which platform it's working? Also how to use rest api to download health kit csv files liked to each identifier ?
error when trying to download from linux
```
SynapseHTTPError: 400 Client Error:
org.sagebionetworks.table.query.ParseException: Encountered " "BP_DATA "" at line 1, column 42.
Was expecting one of:
"AS" ...
"FROM" ...
"*" ...
"-" ...
"+" ...
"/" ...
"%" ...
"DIV" ...
"," ...
``` hey is it possible to run synapse in Linux? (https://www.synapse.org/#!Synapse:syn11269541/discussion/threadId=5437&replyId=18460) I tried it and dint able to perform the query. I got some weird error.
. Is it possible to download in Linux?
Also, I want to ask another question, What's the difference between 6 minutes walk activity and 6 minutes walk displacement vectors? Is there any description to check and parse tmp files of 6-minute walk tests?
In our repo, we have code examples of how you can use this library to download the files: https://github.com/AshleyLab/myheartcounts Great - thanks. Synapse has programmatic clients that allow for access to these data in R, python, or command line (see help documentation [here](https://docs.synapse.org/)).
An example (for Motion Tracker Table) would be as follows:
```r
require(synapser)
synLogin()
# ONLY GET THE FIRST 20 - CAN USE SAME CODE BUT WITHOUT LIMIT TO GET ALL 43,718 FILES (WILL JUST TAKE LONGER)
aa <- synTableQuery('SELECT * FROM syn16782059 LIMIT 20')
df <- as.data.frame(aa)
dataFiles <- synDownloadTableColumns(aa, "data.csv")
# MATCH LOCAL FILE LOCATION WITH REST OF THE METADATA
df$dataLocation <- dataFiles[ df$data.csv ]
```
I am not sure if I understand you correctly. The files I got have all the data that were mentioned in the paper. Please check the data description page (https://www.synapse.org/#!Synapse:syn11269541/wiki/588018). The largest 2 files that I got was ~17 & 20 MB (a total of 136536 rows). The rest of the files: 1-5MB). By the way, there were no heart rate data available in any of those files since most of the data were acquired using the smartphones. In any case, I believe the researcher who added the data can answer your question accurately. Thanks. Thanks for your reply. The export table in the "Download Options" only downloads the table in view not the actual data that is in the data.csv for each row entry/individual. I am not sure if there is any bulk download option available. But you can use the export table in the 'Download Options' tab to get all the data in the csv file. That means you can get all the data by clicking export tables for all the tables headers (15 in total, e.g., Day one survey, HealthKitData, Six-minute walk activity, etc). By the way, some of the individual data files are with the 'tmp' format which may not be accessible using the application like notepad or wordpad.
I have a question. In Motion Tracker data file, there are numbers under the data.csv header. Please share if you know whom these data belong to.
Thanks.