This project is mirrored from https://*****@github.com/RNAcentral/rnacentral-webcode.git. Pull mirroring updated .
  1. 07 Apr, 2021 1 commit
  2. 04 Apr, 2018 1 commit
  3. 06 Mar, 2018 1 commit
    • Blake Sweeney's avatar
      Remove extra Rfam based naming · a858a3af
      Blake Sweeney authored
      This prevents the code from using rfam as a source of names in cases
      where Rfam may have a better name than the selected database. The idea
      was to use an Rfam name if the name had 'predicted' in it. However, this
      lead to problems where Rfam and the database disagreed on what RNA type
      the sequence is. This is fixable, but I am skipping it for now.
      a858a3af
  4. 01 Mar, 2018 2 commits
  5. 28 Feb, 2018 1 commit
    • Blake Sweeney's avatar
      Update tests and naming logic · 092ef960
      Blake Sweeney authored
      This updates the naming logic and tests. We add more tests to ensure
      that some issues/sequences that were shown in the SAB will always have
      the correct naming. Additionally, I've changed some logic to better
      handle certain edge cases. For example if we have a sequence named
      'predicted', we now try to find an Rfam sequence and then use that
      sequence along with any gene annotation. Hopefully this improves the
      naming of other cases.
      092ef960
  6. 15 Nov, 2017 1 commit
  7. 10 Nov, 2017 1 commit
  8. 26 Sep, 2017 2 commits
    • Blake Sweeney's avatar
      Improve HGNC and mirBase naming · 2e8914ef
      Blake Sweeney authored
      In both databases it is possible for more than one gene/precursor to map
      to a single URS. In this case we need to use a better naming system than
      the current one. Notably we should indicate if there are several items.
      This means listing the genes/precursors or a note to say there is more
      than one. This adds some logic to do so. It includes logic to do things
      like correctly sort names (basically stripping trailing numbers if
      possible) so things are listed in the right order. The code is rather
      obscure at the moment but can be corrected.
      2e8914ef
    • Blake Sweeney's avatar
      First attempt at correcting HGNC descriptions · 7d81099a
      Blake Sweeney authored
      HGNC had some useful suggestions on changes the naming scheme they want.
      First, they don't want us to select high gene numbers (which was an
      accident) like RNA5S17 instead of RNA5S1. This should be done by
      selecting descriptions from accessions with the smallest gene.
      
      Also, for URS that represent more than one gene they want an indication
      of that. So I've added a list of the genes if there are few (< 3) and
      otherwise the text 'multiple genes' will appear. Untested, so far but
      this is the general approach.
      
      I've also altered the default behavior to bias it away from larger gene
      numbers and toward smaller ones, hopefully.
      7d81099a
  9. 25 Sep, 2017 1 commit
    • Blake Sweeney's avatar
      First attempt at correcting HGNC descriptions · 5188d9d6
      Blake Sweeney authored
      HGNC had some useful suggestions on changes the naming scheme they want.
      First, they don't want us to select high gene numbers (which was an
      accident) like RNA5S17 instead of RNA5S1. This should be done by
      selecting descriptions from accessions with the smallest gene.
      
      Also, for URS that represent more than one gene they want an indication
      of that. So I've added a list of the genes if there are few (< 3) and
      otherwise the text 'multiple genes' will appear. Untested, so far but
      this is the general approach.
      
      I've also altered the default behavior to bias it away from larger gene
      numbers and toward smaller ones, hopefully.
      5188d9d6
  10. 14 Aug, 2017 2 commits
  11. 06 Mar, 2017 3 commits
  12. 20 Jan, 2017 4 commits
    • Blake Sweeney's avatar
      Make better use of django ORM for speed · 2530ca78
      Blake Sweeney authored
      The ORM can be much faster than it was before. This reduces the run time
      of the largest case I test (10k xrefs) to ~3 seconds. Previously it
      could take a long time (minutes) to compute the description. This was
      due to inefficient usage of the ORM where it basically had to select
      each xref one at a time, leading to many queries. We now do a better job
      of using the ORM and querying to be much faster.
      
      This is a large improvement over the previous method. While I have
      tested raw sql and get ~1 second for run time, it is not worth the
      addition of raw sql strings into our code base.
      
      To make this possible I refactored the get_description/get_rna_type
      functions slightly to take the list of xrefs as input and moved the
      valid_xref method into the Rna model. This version should cover all the
      basic functionality we need to improve naming.
      2530ca78
    • Blake Sweeney's avatar
      Rename tests and alter limits · b41fa3b2
      Blake Sweeney authored
      The test methods were badly named. Also I now allow upto 5 queries. This
      is still very few.
      b41fa3b2
    • Blake Sweeney's avatar
      Add django-performance-testing · 35ce8a09
      Blake Sweeney authored
      This is useful for constraining the runtime and the number of queries
      issued in tests. This is helpful when dealing with the sequences that
      many xrefs. By using this I can test that the number of queries are
      small.
      35ce8a09
    • Blake Sweeney's avatar
      Pass all tests · c0807a67
      Blake Sweeney authored
      This now handles all cases (excluding the one expected failure). The
      failure is because of uncertainty over the rna_type, which will be
      resolved once more databases are installed.
      
      I have had to change a few tests to match the descriptions but overall
      we now pass all tests and show the expected behaviors. However, the code
      is very slow due to far too many database queries. This needs to be
      cleaned up and fixed.
      c0807a67
  13. 19 Jan, 2017 4 commits
  14. 18 Jan, 2017 1 commit
    • Blake Sweeney's avatar
      Add some tests for naming · ccdd5329
      Blake Sweeney authored
      These test probably don't run yet but exist for me to outline the
      behaviors I want. The idea is to get a bunch of examples of naming that
      I like and then ensure the code matches it. So far this just comes from
      me browsing the site be eventually we should include examples from
      people who found issues.
      ccdd5329