Count cases per region in the original Danish metadata and filter microreact output accordingly

[tomersagi]

• [x] Find the Danish full-case-list @tomersagi
• [x] Change the output query to output single cases @tomersagi
• [x] Write a script to count the cases by week and region. @miro
• [x] Use this count in our to_microreact script to filter out region-week cases with less than 3 cases (reduce to 0) @miro

[tomersagi]

Danish full-case-list file is an Excel file. You can now access this filepath using the config file parameter named 'raw_ssi_file'.

[tomersagi]

Header of csv file created from the xlsx file:

Casedefinition,EpiLBnr,SampleDate,CPR,FirstName,LastName,Sex,Address,ZipCodeCity,NUTS3Text,NUTS3Code,Region,KMA,Applicant,SymptomsStartDate,Symptoms,Travel,CountryOfTravel,PlaceOfInfection_EN,PlaceOfInfection_DA,ContactWithCase,Occupation,LastUpdateEpiMiBa,SampleAge,SampleAgeGrp,ReportAge,ReportAgeGrp,EpilprResp_start,EpilprResp,EpilprVent_start,EpilprVent,EpilprECMO_start,EpilprECMO,EpilprHeart,EpilprHeart_start,Diabet,Neuro,Cancer,Adipos,Nyre,Haem_c,Card_dis,Resp_dis,Immu_dis,Other_risk,CodR_DateOfDeath,CodR_Death60Days,CPR_Death60Days,CPR_DateOfDeath,Parishcode,ParishName,batchId,Timestamp,CodR_Death30Days,CPR_Death30Days,DateOfDeath_final,Death60Days_final,Death30Days_final,CitizenshipCode,CitizenshipText,MunicipalityCode,EpiLPRFirstAdm,EpiLPRFirst_in,EpiLPRFirst_out,EpiLPRLastAdm,EpiLPRLast_in,EpiLPRLast_out,EpiLprICU_in,EpiLprICU_out,EpilprICT,EpilprICT_start,RegAdmission,Reg_RegionCode,RegHospital,RegDepartment,RegICU,Speciality,RegReport_time,COVID19_Status,COVID19_EndDate,COVID19_rule,Pregnancy,Doctor,Nurse,HealthAssist,NewlyAdmDate,newlyAdm,LastDsc,LastAdm,FirstDsc,FirstAdm,RegLast_out,RegLast_in,RegFirst_out,RegFirst_in,RegRespICU,Tilhorsforhold,Tilhorsland,Plejehjem,PlejehjemsId,Plejehjemsnavn,branche1,branche2,branche3,ICUAdm,ICUDsc,Plejehjem_doed,RegFirstICU_in,RegFirstICU_out,DREAM_kom,DREAM_reg,TilhorsRegion,TilhorsClassification,Coordinate_x,Coordinate_y,plejehjem_sampledate,Plejehjem_date,iTESTCENTER

[tomersagi]

You can count the cases by using the SampleDate and NUTS3Code fields

[tomersagi]

• [ ] put the filtered cases as anonymous cases at the end of the tsv file