Add fio2_percent and oxygen_flow_rate

[pipliggins]

No description provided.

[ekamau]

thanks @pipliggins - lots of work!
all look very good; and just a few minor changes to look at ..

[pipliggins]

@sadiekelly would you mind checking the guinea parser particularly? It seems like it was merged before your review changes were applied, so it's worth going back and double checking I caught everything.

[sadiekelly]

@pipliggins I think for creating the works_lab supertype we'd only map the Y responses if the question specifically asks about working in a microbiology lab, as someone could respond 'N' to not working in a microbiology lab but they are still a lab worker, what do you think?

[pipliggins]

@sadiekelly so you mean if a question asks 'are you a microbiology worker?' we'd only map the yes responses to works_lab, but both Y and N for works_microbiology_lab? Yes, I think that makes sense. We might potentially need to consider this logic for other super types as well...

[sadiekelly]

yes, that's right, I think that's the best way. Which of the other super types are you thinking of?

[pipliggins]

I haven't thought it through... but possibly for things like oxygen therapy - @abhidg remind me, if a 'false' response is given within combinedType = any, will that override a 'True' response from earlier?

[pipliggins]

@sadiekelly with the 2 new definitions here (oxygen_flow_rate and fio2) - do you think the presence of either/both should be used as an indicator of oxygen therapy in the visit table? Or just one?

[github-actions]

Summary of the missing optional fields for the ccp-cameroon parser:

table	missing	total_fields	percentage_coverage
subject	17	56	69.642857%
visit	26	53	50.943396%
observation	29	70	58.571429%

SUBJECT                                         
dataset_id                                      False
sex_at_birth                                    False
ethnicity                                       False
works_microbiology_lab                          False
pregnancy_date_of_delivery                      False
pregnancy_post_partum                           False
preterm_infant                                  False
has_asplenia                                    False
has_chronic_respiratory_disease                 False
diabetes_type                                   False
has_apnoea                                      False
has_inflammatory_bowel_disease                  False
has_rare_disease_inborn_metabolism_error        False
has_solid_organ_transplant                      False
has_tuberculosis_past                           False
has_hiv_art                                     False
has_immunosuppression                           False
VISIT                                           
dataset_id                                      False
phase                                           False
treatment_corticosteroid_type                   False
treatment_corticosteroid_type_other             False
treatment_oxygen_mask_prongs                    False
treatment_antifungal_agent_type                 False
treatment_antibiotics_type                      False
treatment_anticoagulation                       False
treatment_ace_inhibitors                        False
treatment_arb                                   False
treatment_antimalarial_type                     False
treatment_high_flow_nasal_cannula               False
treatment_steroids                              False
treatment_immunosuppressant                     False
treatment_intravenous_fluids                    False
treatment_nsaid                                 False
treatment_neuromuscular_blocking_agents         False
treatment_cpr                                   False
treatment_offlabel                              False
treatment_respiratory_support                   False
treatment_colchicine                            False
treatment_immunoglobulins                       False
treatment_delirium                              False
treatment_delirium_type                         False
treatment_monoclonal_antibody                   False
treatment_pacing                                False
OBSERVATION                                     
avpu                                            False
acvpu                                           False
oxygen_flow_rate                                False
oxygen_flow_rate                                False
clinical_classification_critical_illness_scale  False
total_fluid_output_ml                           False
base_excess                                     False
clinical_frailty_score                          False
inability_to_walk_scale                         False
glasgow_coma_score                              False
blantyre_coma_score                             False
mid_upper_arm_circumference_cm                  False
fio2_percent                                    False
pao2_mmHg                                       False
pco2_mmHg                                       False
pH                                              False
richmond_agitation-sedation_scale               False
riker_sedation-agitation_scale                  False
other_symptom                                   False
mean_arterial_blood_pressure_mmHg               False
anorexia                                        False
bleeding                                        False
confusion                                       False
cyanosis                                        False
feeding_intolerance_pediatrics                  False
hepatomegaly                                    False
inability_to_walk                               False
irritability_pediatrics                         False
lung_sounds                                     False
heart_sounds                                    False

[pipliggins]

Hi @sadiekelly, would you mind doing a final check through this? I think I've done everything we've discussed, but a second pair of eyes before I merge would be great!

[sadiekelly]

Hi @sadiekelly, would you mind doing a final check through this? I think I've done everything we've discussed, but a second pair of eyes before I merge would be great!

hi @pipliggins! I've added a few comments on the updated files - let me know if something is not clear - thanks!