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Daily clinical measurements

mwham requested to merge daily_clinical_measurements into master

New data source: clinical_data. Loaded from full ccp_data.csv table. Using this, it should be possible to join LIMS samples to clinical data from the same day, ± a day or two:

isaric=# SELECT distinct view_lims_data."Kit_ID", view_lims_data."Patient_ID", clinical_data.subjid, view_lims_data."Date_Collected", clinical_data.daily_dsstdat, clinical_data.dsterm, clinical_data.daily_invasive_prtrt, clinical_data.daily_fio2_combined FROM isaric.view_lims_data LEFT OUTER JOIN isaric.clinical_data ON canonical_isaric_id = subjid AND "Date_Collected" - daily_dsstdat BETWEEN -1 AND 1 ORDER BY "Kit_ID", subjid, "Date_Collected";
  Kit_ID  | Patient_ID |   subjid   | Date_Collected | daily_dsstdat |  dsterm   | daily_fio2_combined 
----------+------------+------------+----------------+---------------+-----------+---------------------
 CCP0001  | ABCDE001   | ABCDE-0001 | 2020-08-17     | 2020-08-16    |           |                0.21
 CCP0001  | ABCDE001   | ABCDE-0001 | 2020-08-17     | 2020-08-17    |           |                0.28
 CCP0002  | ABCDE001   | ABCDE-0001 | 2020-08-19     | 2020-08-19    | Discharge |                    
 CCP0004  | ABCDE003   | ABCDE-0003 | 2020-08-16     | 2020-08-16    |           |                0.21
 CVRI0003 | ABCDE002   | ABCDE-0002 | 2020-08-16     | 2020-08-16    |           |                0.21
(5 rows)

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