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ga4gh / ga4gh-server

Reference implementation of the APIs defined in ga4gh-schemas. RETIRED 2018-01-24
http://ga4gh.org
Apache License 2.0
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Add "update example data" to release process #1629

Open david4096 opened 7 years ago

david4096 commented 7 years ago

We unfortunately missed this, it should be in the release process docs http://ga4gh-server.readthedocs.io/en/stable/development.html#release-process

CanWood commented 7 years ago

Just found #1563 which covers this. I'll watch that. Cheers!

Original comment: Not sure if this is related, but when following the docs, using the example-data fails. SHould I follow this issue or open anew one? Cheers! ( output follows ):

(ga4gh-env) user@localhost:/srv/ga4gh$ ga4gh_server
Traceback (most recent call last):
  File "/srv/ga4gh/ga4gh-env/bin/ga4gh_server", line 11, in <module>
    sys.exit(server_main())
  File "/srv/ga4gh/ga4gh-env/local/lib/python2.7/site-packages/ga4gh/server/cli/server.py", line 51, in server_main
    parsedArgs.config_file, parsedArgs.config, parsedArgs.port)
  File "/srv/ga4gh/ga4gh-env/local/lib/python2.7/site-packages/ga4gh/server/frontend.py", line 296, in configure
    app.backend = _configure_backend(app)
  File "/srv/ga4gh/ga4gh-env/local/lib/python2.7/site-packages/ga4gh/server/frontend.py", line 259, in _configure_backend
    dataRepository.open(datarepo.MODE_READ)
  File "/srv/ga4gh/ga4gh-env/local/lib/python2.7/site-packages/ga4gh/server/datarepo.py", line 618, in open
    self.load()
  File "/srv/ga4gh/ga4gh-env/local/lib/python2.7/site-packages/ga4gh/server/datarepo.py", line 1425, in load
    self._readSystemTable()
  File "/srv/ga4gh/ga4gh-env/local/lib/python2.7/site-packages/ga4gh/server/datarepo.py", line 744, in _readSystemTable
    raise exceptions.RepoInvalidDatabaseException(self._dbFilename)
ga4gh.server.exceptions.RepoInvalidDatabaseException: Database file 'ga4gh-example-data/registry.db' is malformed.  Either change the configuration to point to a valid file or create one using the repo manager.