500 Server Error when storing new version of file from command line

Description

Using the command line client to store new version of already existing file returns a SynapseHTTPError:

synapse store C4_PCBC_CV_Ontology_For_Synapse.csv
..,!!
Upload completed in 2 seconds.

SynapseHTTPError: 500 Server Error: Internal Server Error
Send a Jira bug report to the platform team with this message: java.lang.NullPointerException
at java.net.URLDecoder.decode(URLDecoder.java:136)
at org.sagebionetworks.repo.model.jdo.KeyFactory.urlDecode(KeyFactory.java:63)
at org.sagebionetworks.repo.model.jdo.KeyFactory.stringToKey(KeyFactory.java:48)
at org.sag

Showing that file says it doesn't exist:

[kdaily@localhost data]$ synapse show C4_PCBC_CV_Ontology_For_Synapse.csv | les

SynapseError: File not found in Synapse

However, listing the directory in which it resides shows the file:

[kdaily@localhost data]$ synapse list syn2755407 -r
syn2755407 data/
syn2759310 C4_PCBC_CV_Ontology_Categories_For_Synapse.csv
syn2758116 C4_PCBC_CV_Ontology_For_Synapse.csv
syn2755413 C4_PCBC_MetaData_Terms_For_Synapse.csv
syn2755408 C4_PCBC_Synapse_MetaData_Terms.xlsx

The web client shows a number of recent uploads, but none have the changes made to the file.

Environment

None

Activity

Show:
Kenneth Daily
October 13, 2014, 5:22 PM

Maybe I'm using client wrong (without specifying --parentid), as I successfully stored the problem file by specifying it.

However, I got no error when storing a different file without specifying --parentid.

Chris Bare
October 13, 2014, 5:57 PM

Hi Kenneth,

These are legitimate bugs: for one we should give better feedback and the 500 error is a bug for sure, though on which side I don't know.

As you figured out, you should be doing the following:

Thanks for the bug report!

Chris Bare
October 13, 2014, 6:25 PM

Three subparts this:

  • synapse store <filename> stores using the root node (syn4489) as the parent, which should be prevented.

  • Investigate how the 500 comes about

  • The issue with synapse show is probably just making clear what's happening (not found based on MD5, I'm guessing.)

Chris Bare
August 11, 2016, 12:05 AM

I think this just needs validation?

Kenneth Daily
September 8, 2016, 10:50 PM

Confirmed - client requires parentId now.

Assignee

Chris Bare

Reporter

Kenneth Daily

Labels

None

Validator

Kenneth Daily

Development Area

None

Release Version History

None

Components

Fix versions

Affects versions

Priority

Major
Configure