fhirbuild

build fhir jsons from code or csv.

usage:

fhirbuild <observation|specimen|patient> <in csv> <out dir> <-d delimiter input> <-e encoding input>

example:

fhirbuild observation GSA_prep\out\gsa-korr.csv tmp-dir -d ; -e utf-8-sig

column names

csv input column names for building an primary (master) or aliquot (derived) specimen:

category: [MASTER|DERIVED]    is the sample primary (MASTER) or
                              aliquot (DERIVED)?
collection_date               the collection date (entnahmedatum)
concentration                 the concentration
concentration_unit            the unit of the concentration
derival_date                  the derival date (aufteilungsdatum) is the
                              same as "datum der ersten einlagerung"
fhirid                        the identifier specific to fhir
idcs_[SAMPLEID|EXTSAMPLEID|...] one or more ids
initial_amount                the initial amount
initial_unit                  the initial unit
location_path                 the location path
organization_unit             the organization unit
parent_fhirid                 for an aliquot, link to the fhirid
                              of the parent aliquotgroup
received_date                 the received date (eingangsdatum)
receptacle                    the receptacle (probenbehaelter). becomes container.
reposition_date               the reposition date (einlagerungsdatum)
rest_amount                   the rest amount
rest_unit                     the unit of the rest amount
subject_limspsn               the limspsn of the patient
type                          the sample's type (material, CIT etc)
xpos                          the x position on the rack
ypos                          the y position on the rack

todo centrifugation values

csv input column names for aliquotgroup:

category: ALIQUOTGROUP        the category of the sample
fhirid                        the identifier specific to fhir
organization_unit             the organization unit
parent_sampleid               for an aliquotgroup, link to the sampleid
                              of the group's parent primary sample
received_date                 the received date (eingangsdatum)
subject_limspsn               the limspsn of the patient
type                          the sample's type (material, CIT etc)

csv input column names for observation:

cmp_[...]                     put your messwerte codes here, one column
                              per code, each prefixed with 'cmp_' (for component
                              field in fhir)
effective_date_time           sollte das datetime heissen?
id_[SAMPLEID|EXTSAMPLEID|...] a sample id
methodname                    the messprofile name
method                        the messprofile code
sender                        the EINS_CODE
subject_psn                   a patient id

csv input columns for patient:

idcp_[PSN|LIMSPSN...]
fhirid
organization_unit
study

build and install

build:

pip install build
python3 -m build

install:

pip install dist/fhirbuild-<current-version>.whl

dev

fhir examples for master (primary), aliquotgroup and derived (aliquot) are in in example.md.

todo

patient building with id and studienzugeheorigkeit

primary to child relationship