馃悰
馃摑 Describe the Issue
We made an assumption that basespace_sample_id and basespace_sample_name would be the same. We just ran into a scenario where this is not the case, which caused BaseSpace_Fetch_PHB to fail on the latest version (v4.1.0).
From our discovery, when a user has discrepant basespace_sample_id and basespace_sample_name inputs, the grep on line https://github.com/theiagen/public_health_bioinformatics/blob/main/tasks/utilities/data_import/task_basespace_cli.wdl#L49 fails to pull the dataset ID. But when the two inputs are congruent with one another, it works.
Alternatively, we need to ensure that labs are making these two inputs the same. I would greatly appreciate any guidance on how we should handle this.
Important note: This could also probably happen if the user uses project_id to search on line https://github.com/theiagen/public_health_bioinformatics/blob/main/tasks/utilities/data_import/task_basespace_cli.wdl#L58
馃捇 Version Information
PHB v4.1.0
Works on PHB v3.0.0
馃悰
馃摑 Describe the Issue
We made an assumption that
basespace_sample_idandbasespace_sample_namewould be the same. We just ran into a scenario where this is not the case, which caused BaseSpace_Fetch_PHB to fail on the latest version (v4.1.0).From our discovery, when a user has discrepant
basespace_sample_idandbasespace_sample_nameinputs, the grep on line https://github.com/theiagen/public_health_bioinformatics/blob/main/tasks/utilities/data_import/task_basespace_cli.wdl#L49 fails to pull the dataset ID. But when the two inputs are congruent with one another, it works.Alternatively, we need to ensure that labs are making these two inputs the same. I would greatly appreciate any guidance on how we should handle this.
Important note: This could also probably happen if the user uses project_id to search on line https://github.com/theiagen/public_health_bioinformatics/blob/main/tasks/utilities/data_import/task_basespace_cli.wdl#L58
馃捇 Version Information
PHB v4.1.0
Works on PHB v3.0.0