Error in sqlite table column reading by chanjo report

[kevjp]

Following the upgrade suggested in #22 I still am running into problems when I run the command:

chanjo report --render pdf --samples "sample2" > ./out.pdf

This time the error report is:

[2016-03-09 17:17:11,092] INFO    : chanjo.cli.root          : version 3.4.1
--------------------------------------------------------------------------------
DEBUG in api [/usr/local/lib/python2.7/dist-packages/chanjo/store/api.py:45]:
set up new session
--------------------------------------------------------------------------------
[2016-03-09 17:17:11,450] ERROR   : chanjo_report.server.blueprints.report.views: (pysqlite2.dbapi2.OperationalError) no such column: sample.source [SQL: u'SELECT sample.id AS sample_id, sample.group_id AS sample_group_id, sample.source AS sample_source, sample.created_at AS sample_created_at \nFROM sample \nWHERE sample.group_id = ?'] [parameters: (u'coverage',)]
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/chanjo_report/server/blueprints/report/views.py", line 45, in map_samples
    samples = {sample_obj.id: sample_obj for sample_obj in query}
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/orm/query.py", line 2736, in __iter__
    return self._execute_and_instances(context)
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/orm/query.py", line 2751, in _execute_and_instances
    result = conn.execute(querycontext.statement, self._params)
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/engine/base.py", line 914, in execute
    return meth(self, multiparams, params)
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection
    return connection._execute_clauseelement(self, multiparams, params)
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/engine/base.py", line 1010, in _execute_clauseelement
    compiled_sql, distilled_params
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/engine/base.py", line 1146, in _execute_context
    context)
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/engine/base.py", line 1341, in _handle_dbapi_exception
    exc_info
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/util/compat.py", line 200, in raise_from_cause
    reraise(type(exception), exception, tb=exc_tb, cause=cause)
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/engine/base.py", line 1139, in _execute_context
    context)
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/engine/default.py", line 450, in do_execute
    cursor.execute(statement, parameters)
OperationalError: (pysqlite2.dbapi2.OperationalError) no such column: sample.source [SQL: u'SELECT sample.id AS sample_id, sample.group_id AS sample_group_id, sample.source AS sample_source, sample.created_at AS sample_created_at \nFROM sample \nWHERE sample.group_id = ?'] [parameters: (u'coverage',)]
Traceback (most recent call last):
  File "/usr/local/bin/chanjo", line 11, in <module>
    sys.exit(root_command())
  File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 716, in __call__
    return self.main(*args, **kwargs)
  File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 696, in main
    rv = self.invoke(ctx)
  File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 1060, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 889, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 534, in invoke
    return callback(*args, **kwargs)
  File "/usr/local/lib/python2.7/dist-packages/click/decorators.py", line 17, in new_func
    return f(get_current_context(), *args, **kwargs)
  File "/usr/local/lib/python2.7/dist-packages/chanjo_report/cli/core.py", line 46, in report
    click.echo(render_method(api, options=context.obj))
  File "/usr/local/lib/python2.7/dist-packages/chanjo_report/interfaces/pdf/core.py", line 26, in render_pdf
    return HTML(url).write_pdf()
  File "/usr/local/lib/python2.7/dist-packages/flask_weasyprint/__init__.py", line 182, in HTML
    return _wrapper(weasyprint.HTML, *args, **kwargs)
  File "/usr/local/lib/python2.7/dist-packages/flask_weasyprint/__init__.py", line 165, in _wrapper
    return class_(guess, *args, **kwargs)
  File "/usr/local/lib/python2.7/dist-packages/weasyprint/__init__.py", line 82, in __init__
    with result as (source_type, source, base_url, protocol_encoding):
  File "/usr/lib/python2.7/contextlib.py", line 17, in __enter__
    return self.gen.next()
  File "/usr/local/lib/python2.7/dist-packages/weasyprint/__init__.py", line 290, in _select_source
    with result as result:
  File "/usr/lib/python2.7/contextlib.py", line 17, in __enter__
    return self.gen.next()
  File "/usr/local/lib/python2.7/dist-packages/weasyprint/__init__.py", line 298, in _select_source
    with fetch(url_fetcher, url) as result:
  File "/usr/lib/python2.7/contextlib.py", line 17, in __enter__
    return self.gen.next()
  File "/usr/local/lib/python2.7/dist-packages/weasyprint/urls.py", line 315, in fetch
    raise URLFetchingError('%s: %s' % (name, value) if value else name)
weasyprint.urls.URLFetchingError: ValueError: Flask-WeasyPrint got HTTP status 500 INTERNAL SERVER ERROR for http://localhost/group/coverage

I am just trying this out on the demo data from chanjo to begin. Many thanks @robinandeer for your help with the previous issue.