Update tests for new extract context, add some todos
Update tests for new extract context, add some todos

jeffreyliu3230/scrapi,mehanig/scrapi,mehanig/scrapi,felliott/scrapi,CenterForOpenScience/scrapi,ostwald/scrapi,felliott/scrapi,erinspace/scrapi,fabianvf/scrapi,icereval/scrapi,erinspace/scrapi,fabianvf/scrapi,CenterForOpenScience/scrapi,alexgarciac/scrapi