Validation fixes by johngrimes · Pull Request #115 · kind-lab/mimic-fhir

Syntactic changes to simplify recognition of implicit unpivots

piotrszul

committed

Updating setup details for python package.

piotrszul

committed

Removing leading ' ' from display name ' Black ...' in map_race_omb.sql to fix:

piotrszul

committed

Fixing the codes of unit for respiratory and heart rate in fhir_observation_vitalsigns.sql, to [/min] to fix:

piotrszul

committed

Renaming 'mimic-lab-priority' to 'lab-priority' (as per mimic profile) in the extension url in fhir_observation_labevents.sql to fix:

piotrszul

committed

Removing array wrapping for 'medicationCodeableConcept' in fhir_medication_request.sql to fix:

piotrszul

committed

Adding check for null values to avoid creation of empty object in fhir_medication_administration.sql (request) and fhir_specimen.sql (collection) to fix:

piotrszul

committed

Only generate the hasMember array if there is at last one non-NULL reference (mi_ORGANISM) present in fhir_observation_micro_test.sql to fix:

piotrszul

committed

Adding http://www.w3.org/1999/xhtml namespace to the <div> element in medication_mix.sql to fix:

piotrszul

committed

Changing the json export format to 'csv' to fix the backslash escaping issue:

piotrszul

committed

Adding correct null handling for bp vital signs observations in fhir_observation_vitalsigns.sql to conform with http://hl7.org/fhir/StructureDefinition/bp|4.0 . Always producing the required bp comp…

piotrszul

committed

Changing extraction of quantity from pharmacy.fill_quantity. When possible extract the numerical value and the unit. Otherwise, do not provide the quantity.

piotrszul

committed

Correcting display name for loinc code: 2708-6 in fhir_observation_vitalsigns.sql to fix:

piotrszul

committed

Producing NULL for blank dose_given_unit in fhir_medication_administration.sql to fix:

piotrszul

committed

Producing NULL for blank lab_VALUE in fhir_observation_labevents.sql to fix:

piotrszul

committed

Skipping generation of 'medication_dispense' for pharmacy records with blank medication (treating them same as NULL values) to fix:

piotrszul

committed

Making 'dosageInstruction.timing' to include 'code' or 'repeat' in fhir_medication_dispense.sql to fix:

piotrszul

committed

Replacing repated whitespaces with ' ' in pharmacy.frequency to make it comply with coding whitespacing rules and the cs_medication_frequency code system in fhir_medication_dispense.sql, to fix:

piotrszul

committed

Aligning coding display names in fhir resources with the display names in the code system for cs-diagnosis-icd9, cs-diagnosis-icd10 and cs-medication-etc to fix:

piotrszul

committed

Adding 'emar_detail.product_unit' and 'emar_detail.dose_given_unit' as source sources for cs_unit code system to fix:

piotrszul

committed

Removing the code system and values sets with not sql scripts from terminology description tables.

piotrszul

committed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Validation fixes#115

Commits on Jun 27, 2024

Syntactic changes to simplify recognition of implicit unpivots

Updating setup details for python package.

Removing leading ' ' from display name ' Black ...' in map_race_omb.sql to fix:

Fixing the codes of unit for respiratory and heart rate in fhir_observation_vitalsigns.sql, to [/min] to fix:

Renaming 'mimic-lab-priority' to 'lab-priority' (as per mimic profile) in the extension url in fhir_observation_labevents.sql to fix:

Removing array wrapping for 'medicationCodeableConcept' in fhir_medication_request.sql to fix:

Adding check for null values to avoid creation of empty object in fhir_medication_administration.sql (request) and fhir_specimen.sql (collection) to fix:

Only generate the hasMember array if there is at last one non-NULL reference (mi_ORGANISM) present in fhir_observation_micro_test.sql to fix:

Adding http://www.w3.org/1999/xhtml namespace to the <div> element in medication_mix.sql to fix:

Changing the json export format to 'csv' to fix the backslash escaping issue:

Adding correct null handling for bp vital signs observations in fhir_observation_vitalsigns.sql to conform with http://hl7.org/fhir/StructureDefinition/bp|4.0 . Always producing the required bp comp…

Changing extraction of quantity from pharmacy.fill_quantity. When possible extract the numerical value and the unit. Otherwise, do not provide the quantity.

Correcting display name for loinc code: 2708-6 in fhir_observation_vitalsigns.sql to fix:

Producing NULL for blank dose_given_unit in fhir_medication_administration.sql to fix:

Producing NULL for blank lab_VALUE in fhir_observation_labevents.sql to fix:

Skipping generation of 'medication_dispense' for pharmacy records with blank medication (treating them same as NULL values) to fix:

Making 'dosageInstruction.timing' to include 'code' or 'repeat' in fhir_medication_dispense.sql to fix:

Replacing repated whitespaces with ' ' in pharmacy.frequency to make it comply with coding whitespacing rules and the cs_medication_frequency code system in fhir_medication_dispense.sql, to fix:

Aligning coding display names in fhir resources with the display names in the code system for cs-diagnosis-icd9, cs-diagnosis-icd10 and cs-medication-etc to fix:

Adding 'emar_detail.product_unit' and 'emar_detail.dose_given_unit' as source sources for cs_unit code system to fix:

Removing the code system and values sets with not sql scripts from terminology description tables.

Commits on Jun 28, 2024

Adding the python script for generating code systems and value set resorces from mimic database (fhir_trm schema).

Switching mimic-profiles to the aehrc repo with updated terminlogy resources