Sara offboarding

[SaraKoskelainen]

Tasks related to Sara leaving the group

General

• [x] Share with Vincent the awk script to set omit 2 values for selected endpoints in the Risteys endpoint definition file: set_omit_value_for_selected_endpoints.awk. The script adds omit 2 value for endpoints that have omit 2 value in the definition file (used by Andrius to generate the FinRegistry endpoints) but those endpoints are not included in the omitted endpoints file shared with Vincent by THL registry team because the that file only included newly added omit endpoint, not all of them.

• [x] #229

  • [x] make authentification work
  • [x] make results to show
    • [x] GWS results slightly differ between FR-FG Risteys and FinnGen Risteys. This might be because Vincent seemd to use updated input correlation file. --> fix
    • [x] --> test
  • [x] --> release & test --> codebase deployed but not taking any traffic atm
  • [x] --> push code changes to GitHub in FR_FG_WIP_coloc_hits_links branch & GitLab (GC OAuth credentials)
  • [x] TODO: Make sure authorization is correctly done and proper testing

• [x] update FR-FG Risetys GitHub README documentation

  • [x] R10 data. NOTE, FinnGen genes file not added to file documentation because coloc hits links not deployed yet.
  • [x] The link to ”Kela Kansallinen koodistopalvelu” seems to be incorrect, Safari don’t open the page and says that “This connection is not private”

• [x] remove GitHub automatic tests against removed sections (failed commits)

• [x] push secret credentials to GitLab!

  • [x] DB credentials
  • [x] user authentification Google credentials

• [x] Check handling of _EXALLC and _EXMORE endpoints in FinRegistry results

  • [x] R script for modifying the FinRegistry input data to have results for _EXALLC & _EXMORE endpoints was already saved to pipeline directory in codebase: https://github.com/dsgelab/risteys/blob/FR_FG/pipeline/copy_results_for_EXALLC_and_EXMORE_endpoints_FR_r10.R
  • [x] check with Vincent the awk scripts used for creating file of _EXALLC & _EXMORE endpoint names and checking how many _EXALLC & _EXMORE endpoints will not have results if copying from counterpart endpoints, because counterpart endpoints in some cases are omitted endpoints.

• [x] check if there's some other modification done to data outside pipeline

• [x] save datafiles to Google Cloud storage

  • [x] first make sure what is the correct correlation file
  • [x] also endpoints_EXMORE_core_not_omit_2_r10.csv & endpoints_EXALLC_core_not_omit_2_r10.csv that were used as an input for copy_results_for_EXALLC_and_EXMORE_endpoints_FR_r10.R script

• [x] clean codebase: remove forgotten printings from endpoint explainer section

• [x] document how fr excluded endpoint list was generated --> create_excl_endpoints_list.R & import_excluded_endpoints.exs

• [x] share possibly important notes to Vincent

  • [x] data import notes
  • [x] Relationships section notes

• [x] #230

• [x] Should we ask FR-FG Risteys to be added in Finngen.fi/us/members/dashboard > Tools and Resources > Risteys? Vincent: cancelled, as the FG-only portal is now redirecting to FR+FG

Previously planned/ suggested updates/ improvements:

• [x] #233

• [x] user-agent issue in Relationships table

  • Essi: maybe it's name field -> maybe named as name or something -> browser tries to be smart about it
  • Vincent: Cancelling this one, as low-impact.

• [x] have proper tests for Relationships section

  • Vincent: Cancelling this one as too vague.

• [ ] Have FinRegistry results in the Relationship section for _EXMORE and _EXALLC endpoints. These are not currently available as FinRegistry endpoints are run without generation of _EXMORE and _EXALLC endpoints and thus results need to be manually copied from the counterpart endpoints that have exactly the same cases (and also controls in FinRegistry data because there are no specific rules used for controls in FinRegistry).

• [ ] There are endpoints that are priority endpoints but also non-core endpoints: e.g. C3_CANCER, C3_PANCREAS, C3_THYROID_GLAND. (For the EXALLC and EXMORE endpoints could copy FinRegisty from the endpoint non-EXALLC and EXMORE counterparts. This is not currently done for survival analysis results in the Relationships table. See above point.)

• [x] Improve endpoint search

  • Vincent: Cancelling this one as too vague, unclear next step.

• [x] Make the random endpoint button to return only meaningful endpoints, e.g. non-omitted endpoints only

  • Vincent: Cancelling this one, as it is useful to sometimes get ommited endpoints: good for debugging, good because sometimes users will run into this pages with other means.

• [ ] Allow downloading data showed in the Relationships table

Comments and suggestions by Andrea:

• [ ] documentation page

  • [ ] add sample size of FinRegisty to doc page
  • [x] have tutorial, similar to what's in FinnGen Risteys
    • Vincent: Marking this one as duplicate of #222

• [ ] ontology: check with Essi to have the latest desciptions in use

• [ ] summary stats titles: add project name after each subtitle instead of having project names in the beginnig of the section

• [ ] color coding for FR and FG results: one color for both projects and use those across the endpoint page

  • [ ] only one color in cumulative incidence plot
  • [ ] histograms in color
  • [ ] titles in colors

• [ ] Mortality help:

  • [ ] help box: add space before the reference to docs: "See Documentation for more details on how xx and xx are computed"
  • [ ] add a color or border to the age button

• [ ] Introduce FR and FG abbreviations

• [ ] Relationships section:

  • [ ] rename GWS to "genome-wide significant"
  • [ ] clarify FG & FR somewhere somehow
  • [ ] Case overlap: try to figure out how to make more clear which values are N & jaccard index
  • [ ] help info box: make titles more prominent
  • [ ] Sara's suggestion: make an extremity plot to compare only other results that are significant or even nominally significant -> Andrea: good idea, need to think about it more closely

[vincent-octo]

Thanks Sara, that will be very useful :)

[vincent-octo]

Putting in Todo as this is a meta-task.