I am denied access to the chr8 vcf file, syn11714197, found here,
https://www.synapse.org/#!Synapse:syn11707420
A few weeks ago my access permissions were sufficient to download the chr19 vcf.gz and tbi file.
It is disappointing that those access permissions no longer apply.
The accompanying tabix file, syn11714097, downloaded fine. I notice that both files have a 3/20/2021 timestamp - perhaps when the files were updated, access permissions went obsolete?
Here is my python console from the failure, using Jordan Kang?s fixed docker image from a few weeks ago.
I tried to follow the suggestion provided (switch to the website, request an update to my access permissions, but I abandoned that once I saw that it was a repetition of what we did a few weeks ago.
````
sudo docker run -it --entrypoint /bin/bash -v /tmp/docker-paul:/tmp docker.synapse.org/syn25326461/synpy-1128
DOCKER.synapsePythonClient> python3
python3
Python 3.6.9 (default, Jan 26 2021, 15:33:00)
>>> import synapseclient
>>> syn = synapseclient.login("paul-shannon", password=?xxxx")
>>> x = syn.get('syn11714097', downloadLocation="/tmp")
x = syn.get('syn11714097', downloadLocation="/tmp")
Downloading [####################]100.00% 140.8kB/140.8kB (708.2kB/s) NIA_JG_1898_samples_GRM_WGS_b37_JointAnalysis01_2017-12-08_8.recalibrated_variants.vcf.gz.tbi Done?
>>> x = syn.get('syn11714197', downloadLocation="/tmp")
x = syn.get('syn11714197', downloadLocation="/tmp")
Traceback (most recent call last):
File "", line 1, in
File "/synapsePythonClient/synapseclient/client.py", line 711, in get
self._check_entity_restrictions(bundle['restrictionInformation'], entity, kwargs.get('downloadFile', True))
File "/synapsePythonClient/synapseclient/client.py", line 721, in _check_entity_restrictions
raise SynapseUnmetAccessRestrictions(warning_message)
synapseclient.core.exceptions.SynapseUnmetAccessRestrictions:
This entity has access restrictions. Please visit the web page for this entity (syn.onweb("syn11714197")). Click the downward pointing arrow next to the file's name to review and fulfill its download require$
````
Created by Paul Shannon paul-shannon This is entirely my error. I had the wrong synid, from the wrong project.
I apologize for taking up your time. And I thank you for the patience you showed.
- Paul @paul-shannon I wonder if you may have inadvertently added a file from the PsychENCODE consortium to your download list
@paul-shannon Hi Paul - it looks like the file you can access is part of the general AD Knowledge Portal, but the file you cannot access is part of the PsychENCODE portal. PsychENCODE requires a slightly different data access application process for you to gain access to the data, described [here](https://www.synapse.org/#!Synapse:syn4921369/wiki/477467). Have you already gone through the data access request process for PsychENCODE, specifically? Thanks, @Mette.
You can see those in my original post, here again for convenience.
Success #1, the tabix file
```
x = syn.get('syn11714097', downloadLocation="/tmp")
Downloading [####################]100.00% 140.8kB/140.8kB (708.2kB/s) NIA_JG_1898_samples_GRM_WGS_b37_JointAnalysis01_2017-12-08_8.recalibrated_variants.vcf.gz.tbi Done?
```
Failure #1, the vcf.gz file
```
x = syn.get('syn11714197', downloadLocation="/tmp")
This entity has access restrictions. Please visit the web page for this entity (syn.onweb("syn11714197")).
```
Success #2, the 15G vcf.gz file, same project, same login and password, same session.
```
x = syn.get('syn11714133', downloadLocation="/tmp")
Downloading [####################]100.00% 14.9GB/14.9GB (49.4MB/s) NIA_JG_1898_samples_GRM_WGS_b37_JointAnalysis01_2017-12-08_19.recalibrated_variants.vcf.gz.synapse_download_74048232 Done...
```
@paul-shannon can you post the synID for the file you can, and one that you can't download @Mette @brucehoff
Thanks for the speedy response.
"Request access" leads to a web form which asks me, among other things, to describe my project.: project lead, institution, intended data use statement That make sense for initial use. Does it make sense here?
I ask because I I still have full access to chr19 vcf.gz, from the same directory, from the same study - I am running a fresh download successfully right now.
**This suggests that I will need to request access, fill out the form, then wait for approval -- for each new chromosome from the study.** Meanwhile the per chromosome tabix files are unprotected?
Is this the intention? Seems rather awkward to me.
Please click 'request access' and follow the instructions on this page, https://www.synapse.org/#!Synapse:syn11714197. Hi Paul, I don't think anything has changed on our end. This is still under the AD Portal Umbrella DUC. @elang , can you please check if Paul's access has expired
Drop files to upload
recently obtained access permissions seemingly no longer apply to vcf.gz, but tbi downloads fine page is loading…