syncToSynapse not returning

xtYao commented 5 years ago

System: MacOS HIgh Sierra

Problem: syncToSynapse function not returning

Code/output:

library(synapserutils)
Loading required package: synapser

TERMS OF USE NOTICE:
When using Synapse, remember that the terms and conditions of use require that you:
1) Attribute data contributors when discussing these data or results from these data.
2) Not discriminate, identify, or recontact individuals or groups represented by the data.
3) Use and contribute only data de-identified to HIPAA standards.
4) Redistribute data only under these same terms of use.

synLogin()
Welcome, Xiaotong Yao!NULL
syncToSynapse("~/manifest.synapse.txt", dryRun = T)
Validation and upload of: ~/manifest.synapse.txtValidating columns of manifest.....OKValidating tha\ t all paths exist..OKValidating that all files are unique...OKValidating provenance...OKValidating \ that parents exist and are containers...OK==================================================We are \ about to upload 2 files with a total size of 1.2MB. ===============================================\ ===NULL
!> syncToSynapse("~/manifest.synapse.txt")

SessionInfo

!> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] synapserutils_0.1.5 synapser_0.6.56

loaded via a namespace (and not attached):
[1] compiler_3.5.1 R6_2.3.0 tools_3.5.1
[4] codetools_0.2-15 pack_0.1-1 PythonEmbedInR_0.3.34

brucehoff commented 5 years ago

https://sagebionetworks.jira.com/browse/SWC-4862

xtYao commented 5 years ago

Hi Bruce,

Thank you very much, this is very helpful.

I know that NCI or TCGA team is moving the actual storage point away from tcgaftps.nci.nih.gov to some new GDC location right at this moment. They gave us a vague timeline and a pair of new credentials, so that as soon as the data migration is complete I will be asked for the new credentials rather than the NIHEXT before. Now that when I input this old NIHEXT credentials onto the web portal or R API while neither responds might related to the unfinished migration. I will contact NCI again to see if I can obtain some more detailed answer from them. Meanwhile, could you tell me if there's any notification I can receive from Synapse that the new storage location is ready to receive my data through Synapse?

Sincerely appreciate your help, Xiaotong Yao PhD student, Imielinski lab

Weill Cornell Medicine xiy2006@med.cornell.edu

On Sun, May 26, 2019 at 8:26 PM Bruce Hoff notifications@github.com wrote:

https://sagebionetworks.jira.com/browse/SWC-4862

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Sage-Bionetworks/synapserutils/issues/16?email_source=notifications&email_token=ABVYZHIRS6BFJI47BSOWE2TPXMTDTA5CNFSM4HPWTKSKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODWIQNVQ#issuecomment-496043734, or mute the thread https://github.com/notifications/unsubscribe-auth/ABVYZHO72OMZLUQ4WQRDWB3PXMTDTANCNFSM4HPWTKSA .

brucehoff commented 5 years ago

Dear Xiaotong: I have made an inquiry and will pass along what I hear back.

larssono commented 5 years ago

Hi Xiaotong: What project are you trying to upload to? Have you tried increasing the debug level to get additional feedback of where syncToSynapse is hanging?

brucehoff commented 5 years ago

Larsson: There seem to be two parallel email threads. In the other one Xiaotong says:

"Thank you so much for your help. The TCGA coordinator says she can still transfer files by Synapse but my credentials were activated after they started the migration process so even though I used to be able to login to the SFTP storage point directly, it is likely that to upload through Synapse is not enabled. At this point, none of us has much to do except waiting on the migration process to finish. Meanwhile I'll have to ask my colleagues to do the uploading for me."

Does this help? Bruce

On Wed, May 29, 2019 at 9:23 AM Larsson Omberg notifications@github.com wrote:

Hi Xiaotong: What project are you trying to upload to? Have you tried increasing the debug level to get additional feedback of where syncToSynapse is hanging?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Sage-Bionetworks/synapserutils/issues/16?email_source=notifications&email_token=AAMNJWGMUJKXCSVMWELTTY3PX2UXJA5CNFSM4HPWTKSKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODWP4BCA#issuecomment-497008776, or mute the thread https://github.com/notifications/unsubscribe-auth/AAMNJWCTSOW43GCCUQX6KS3PX2UXJANCNFSM4HPWTKSA .

brucehoff commented 5 years ago

Per @xtYao:

Thank you so much for your help. The TCGA coordinator says she can still transfer files by Synapse but my credentials were activated after they started the migration process so even though I used to be able to login to the SFTP storage point directly, it is likely that to upload through Synapse is not enabled. At this point, none of us has much to do except waiting on the migration process to finish. Meanwhile I'll have to ask my colleagues to do the uploading for me.

Sage-Bionetworks / synapserutils