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  1. Jun 09, 2016
    • Vermaat's avatar
      Fix data migrations for Reference.source · 67f5d62b
      Vermaat authored
      Due to a bug in the data migrations for the new `Reference.source`
      column introduced in #387 and #392, the start position for references
      created as a slice was used as both start and stop position in the new
      column for storing this data.
      
      This commit fixes these migrations and on top of this adds a new
      migration which corrects any values set by the old migrations (in case
      they were run before this fix). The original columns for these values
      have not yet been dropped, so no data has been lost.
      
      Thanks @ifokkema for reporting this issue.
      
      Fixes #393
      67f5d62b
    • Vermaat's avatar
      Track source for reference files · 1a578b94
      Vermaat authored
      Previously, the original source for a reference file was implicit:
      
      1. If accession number starts with `LRG_`, it came from the LRG FTP
         archive.
      2. If a download URL is known, it was downloaded from there.
      3. If slice data is known, it was sliced from the NCBI.
      4. If a GI number is known, it was downloaded from the NCBI.
      5. Otherwise, it was uploaded.
      
      In preparation for the removal of GI numbers (#349), this had to be
      revisited. We now store the source explicitely in a new `source` field
      on the `Reference` model. If additional information is needed to
      re-fetch the file from this source (e.g., download URL), this is stored
      in a new `source_data` field (always serialized as a string). This
      scheme should be both more explicit and more generic.
      1a578b94
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