Code

R2dt rescan#153

Code

Draft

blakesweeney wants to merge 33 commits intodevRNAcentral/rnacentral-import-pipeline:devfrom r2dt-rescanRNAcentral/rnacentral-import-pipeline:r2dt-rescanCopy head branch name to clipboard

+467-139

Commits

Commits on Oct 25, 2022

• Changes to extract and propagate r2dt version info for hits

  Show description for d0ce5e9
  afg1

  committed
  d0ce5e9

  Copy full SHA for d0ce5e9

• Version information for attempted

  afg1

  committed
  2fd83ff

  Copy full SHA for 2fd83ff

• Tweak workflow to extract and propagate version info

  afg1

  committed
  82e0683

  Copy full SHA for 82e0683

• Remove version from r2dt hit info. It will only be stored in the attempted table now

  afg1

  committed
  3d7c140

  Copy full SHA for 3d7c140

Commits on Oct 26, 2022

• Add cell location as an optional parameter

  afg1

  committed
  d044b85

  Copy full SHA for d044b85

• Rfam cm parser to rnac database entry

  afg1

  committed
  7dd45e8

  Copy full SHA for 7dd45e8

• Fix gtrnadb parser for up to date model spec

  afg1

  committed
  684031b

  Copy full SHA for 684031b

• CM scanner for CRW

  afg1

  committed
  12a0ef3

  Copy full SHA for 12a0ef3

• Working parsers with correct forwarding of db_url

  afg1

  committed
  205efcd

  Copy full SHA for 205efcd

• Use crw metadata file rather than database query and tidy up unused stuff

  afg1

  committed
  54c894e

  Copy full SHA for 54c894e

• Fix RNAse-p parser

  afg1

  committed
  09a8289

  Copy full SHA for 09a8289

• Fix ribovision parser and add lookup for more taxa

  afg1

  committed
  e51c9e1

  Copy full SHA for e51c9e1

• Add metadata url to crw parser

  afg1

  committed
  a29ed6a

  Copy full SHA for a29ed6a

• Fix bad escapes in r2dt version extraction

  afg1

  committed
  7883e8a

  Copy full SHA for 7883e8a

• Workflow to scan the database with r2dt

  Show description for 98537a5
  afg1

  committed
  98537a5

  Copy full SHA for 98537a5

• Update models on conflict

  afg1

  committed
  5e362e1

  Copy full SHA for 5e362e1

• Switch pipeline back to use metadata

  afg1

  committed
  ffa4026

  Copy full SHA for ffa4026

• Fix sed command

  afg1

  committed
  13ff828

  Copy full SHA for 13ff828

• Fix cms paths

  afg1

  committed
  e3485ba

  Copy full SHA for e3485ba

Commits on Oct 27, 2022

• Fix cms path

  afg1

  committed
  9443e2e

  Copy full SHA for 9443e2e

• Add SO term to name lookup and reorganise writing

  afg1

  committed
  cf91e65

  Copy full SHA for cf91e65

• Fix filenames and field names in ctl

  afg1

  committed
  e8aa886

  Copy full SHA for e8aa886

• Add extra parsing to handle LSU and SSU for mt_rRNA

  Show description for 10ee204
  afg1

  committed
  10ee204

  Copy full SHA for 10ee204

Commits on Oct 28, 2022

• Update SO-rnaType name lookup with Rfam types

  afg1

  committed
  30862c9

  Copy full SHA for 30862c9

• Adds another missing type to the mapping

  afg1

  committed
  9faf6c0

  Copy full SHA for 9faf6c0

• Check for .16. in model name properly

  afg1

  committed
  70ec167

  Copy full SHA for 70ec167

Commits on Nov 11, 2022

• Add sequence limit for r2dt processing

  Show description for f06f883
  afg1

  committed
  f06f883

  Copy full SHA for f06f883

• Add some missing SO -> name lookups

  Show description for 6309e33
  afg1

  committed
  6309e33

  Copy full SHA for 6309e33

• Fix model loading ctl to be consistent with table

  Show description for 7cfffea
  afg1

  committed
  7cfffea

  Copy full SHA for 7cfffea

• Pass version correctly to create-attempted

  afg1

  committed
  5df46d3

  Copy full SHA for 5df46d3

• Ignore version in input to publish layout

  afg1

  committed
  34e31c5

  Copy full SHA for 34e31c5

Commits on Nov 14, 2022

• Black reformatting

  afg1

  committed
  8045287

  Copy full SHA for 8045287

Commits on Nov 15, 2022

• Add version invormation to attempted ctl

  afg1

  committed
  b7cd92b

  Copy full SHA for b7cd92b