EVA-1700 — fixes to trait mapping pipeline

[tskir]

• Refactor & code cleanup
  • Traits are now processed in parallel, increasing performance (approx. 8× boost, from 0.5 traits/s to 4 traits/s)
  • Simplify retry policy for json_request, remove unnecessary helpers. Now using an external retry library
  • Configure correct handling of different error types; do not ignore any request errors unless directly specified.
• Fixes for OxO queries
  • OxO requests now always use POST instead of GET
  • Do not try to query OxO when the identifier list is empty, as this causes predictable errors which show up in the logs
  • Correctly handle occasional OxO errors. There is a bug which I discovered and reported: Mapping of Orphanet:121715 results in 500 Internal Server Error EBISPOT/OXO#26
• Logs cleanup
  • Remove double warning for the same error when OLS didn't return a term label
  • Don't show expected OLS query errors for OMIM and MedGen ontologies (since those two are not present in OLS)
  • Demote "OxO no mappings found" from warning to debug level, because this by itself is not an error — OxO does not guarantee that any cross-refs will be found for any particular input term
  • Default logging level is now DEBUG. This provides the most information, while verbose DEBUG entries can be easily filtered out

[coveralls]

Coverage increased (+0.1%) to 74.704% when pulling 27e0588 on tskir:eva-1700-trait-mapping-fixes into a5d53ab on EBIvariation:master.

[tskir]

Merging after one approval as per discussion with @jmmut