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glennhickey / sg2vg

Prototype code for importing a Side Graph (from a GA4GH server) into a VG
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Doesn't Work #1

Closed adamnovak closed 9 years ago

adamnovak commented 9 years ago

I tried this:

./ga2vg http://ec2-54-149-188-244.us-west-2.compute.amazonaws.com/debruijn-sma-k31/v0.6.g | less

And I got this:

Downloading References... (4329 references retrieved)
Downloading Sequences...terminate called after throwing an instance of 'std::runtime_error'
  what():  Error: POST request for Sequences returned {"errorCode": 2023404236, "message": "Request '{u'pageToken': None, u'variantSetId': None, u'referenceSetId': None, u'pageSize': 2147483647}' is not a valid instance of <class 'ga4gh._protocol_definitions.SearchSequencesRequest'>"}

Looks like it's sending bad requests to the server.

glennhickey commented 9 years ago

please hold off using sg2vg for now. it's not finished, and there are graph server issues that need to be resolved (and hence the protocol is in a state of flux).

On Wed, Aug 5, 2015 at 8:10 PM, adamnovak notifications@github.com wrote:

I tried this:

./ga2vg http://ec2-54-149-188-244.us-west-2.compute.amazonaws.com/debruijn-sma-k31/v0.6.g | less

And I got this:

Downloading References... (4329 references retrieved) Downloading Sequences...terminate called after throwing an instance of 'std::runtime_error' what(): Error: POST request for Sequences returned {"errorCode": 2023404236, "message": "Request '{u'pageToken': None, u'variantSetId': None, u'referenceSetId': None, u'pageSize': 2147483647}' is not a valid instance of <class 'ga4gh._protocol_definitions.SearchSequencesRequest'>"}

Looks like it's sending bad requests to the server.

— Reply to this email directly or view it on GitHub https://github.com/glennhickey/sg2vg/issues/1.

glennhickey commented 9 years ago

ok, sg2vg's using the new protocol and passing some basic unit tests. i'm going to look at some integration tests now.

the server still bombs out for anything bigger than brca2, so use at your own risk!

On Thu, Aug 6, 2015 at 9:17 AM, Glenn Hickey glenn.hickey@gmail.com wrote:

please hold off using sg2vg for now. it's not finished, and there are graph server issues that need to be resolved (and hence the protocol is in a state of flux).

On Wed, Aug 5, 2015 at 8:10 PM, adamnovak notifications@github.com wrote:

I tried this:

./ga2vg http://ec2-54-149-188-244.us-west-2.compute.amazonaws.com/debruijn-sma-k31/v0.6.g | less

And I got this:

Downloading References... (4329 references retrieved) Downloading Sequences...terminate called after throwing an instance of 'std::runtime_error' what(): Error: POST request for Sequences returned {"errorCode": 2023404236, "message": "Request '{u'pageToken': None, u'variantSetId': None, u'referenceSetId': None, u'pageSize': 2147483647}' is not a valid instance of <class 'ga4gh._protocol_definitions.SearchSequencesRequest'>"}

Looks like it's sending bad requests to the server.

— Reply to this email directly or view it on GitHub https://github.com/glennhickey/sg2vg/issues/1.

adamnovak commented 9 years ago

OK, it seems to work now. Thanks!