Convert-Pheno
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t/omop2bff/in/mimic_specimen/SPECIMEN.csv
t/omop2bff/in/omop_cdm_eunomia.sql
t/omop2bff/in/PERSON.csv
t/omop2bff/in/README.md
t/omop2bff/out/individuals.json
t/omop2bff/out/individuals_csv.json
t/omop2bff/out/individuals_csv.json.gz
t/omop2bff/out/individuals_drug_exposure.json.gz
t/omop2bff/out/ohdsi.json
t/omop2pxf/out/pxf.json
t/openehr2bff/in/compo_corona.json
t/openehr2bff/in/gecco_personendaten.json
t/openehr2bff/in/gecco_personendaten_patient.json
t/openehr2bff/in/ips_canonical.json
t/openehr2bff/in/laboratory_report.json
t/openehr2bff/in/README.md
t/openehr2bff/out/individuals.json
t/openehr2pxf/out/pxf.json
t/pxf2bff/in/pxf.json
t/pxf2bff/in/pxf.yaml
t/pxf2bff/in/pxf_biosamples.json
share/db/concepts_candidates_2_exposure.csv view on Meta::CPAN
4140933 Seen by occupational health service Observation SNOMED Clinical Finding S "305877000" 2002-01-31 2099-12-31
4136471 Under care of occupational health physician Observation SNOMED Clinical Finding S "305523007" 2002-01-31 2099-12-31
4136492 Under care of community-based occupational therapist Observation SNOMED Clinical Finding S "305606006" 2002-01-31 2099-12-31
4136493 Under care of social services department occupational therapist Observation SNOMED Clinical Finding S "305607002" 2002-01-31 2099-12-31
4138216 Seen by community-based occupational therapist Observation SNOMED Clinical Finding S "305774002" 2002-01-31 2099-12-31
4138217 Seen by social services department occupational therapist Observation SNOMED Clinical Finding S "305775001" 2002-01-31 2099-12-31
4138351 Seen by occupational therapy service Observation SNOMED Clinical Finding S "305852001" 2002-01-31 2099-12-31
46285972 Education on provision of occupational skills training to service user Observation SNOMED Context-dependent S "979391000000102" 2015-10-01 2099-12-31
4263813 Chemotherapy AND/OR radiation therapy prior to lymphadenectomy Observation SNOMED Context-dependent S "396780003" 2003-07-31 2099-12-31
4287023 No chemotherapy AND/OR radiation therapy prior to lymphadenectomy Observation SNOMED Context-dependent S "396781004" 2003-07-31 2099-12-31
756049 History of Suspected exposure (but ruled out after evaluation) to Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the 14 days prior to illness onset Observation OMOP Extension Context-dependent S OMOP4873925 2020-03-18 2099-12-...
756063 History of Animal exposure in the 14 days prior to illness onset Observation OMOP Extension Context-dependent S OMOP4873939 2020-03-18 2099-12-31
756040 History of Close exposure to Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the 14 days prior to illness onset Observation OMOP Extension Context-dependent S OMOP4873943 2020-03-18 2099-12-31
756048 History of Suspected exposure to Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the 14 days prior to illness onset Observation OMOP Extension Context-dependent S OMOP4873923 2020-03-18 2099-12-31
762538 Mother receiving radiation therapy Observation SNOMED Context-dependent S "428641000124103" 2012-09-01 2099-12-31
4079773 Patient advised about exposure to the sun Observation SNOMED Context-dependent S "183079004" 2002-01-31 2099-12-31
4327716 Family history of radiation therapy Observation SNOMED Context-dependent S "430786004" 2008-07-31 2099-12-31
35609834 Daily HIV-PrEP (human immunodeficiency virus pre-exposure prophylaxis) commenced Observation SNOMED Context-dependent S "1086581000000100" 2017-10-01 2099-12-31
35609835 Event-based HIV-PrEP (human immunodeficiency virus pre-exposure prophylaxis) commenced Observation SNOMED Context-dependent S "1086591000000103" 2017-10-01 2099-12-31
35609836 HIV-PrEP (human immunodeficiency virus pre-exposure prophylaxis) declined Observation SNOMED Context-dependent S "1086601000000109" 2017-10-01 2099-12-31
35609855 HIV-PrEP (human immunodeficiency virus pre-exposure prophylaxis) discontinued Observation SNOMED Context-dependent S "1086781000000107" 2017-10-01 2099-12-31
36683665 Fetal exposure to methamphetamine Observation SNOMED Context-dependent S "781699006" 2019-01-31 2099-12-31
36714396 Rabies post exposure prophylaxis contraindicated Observation SNOMED Context-dependent S "719603008" 2017-01-31 2099-12-31
37016704 Assessment of environmental risk done Observation SNOMED Context-dependent S "712805000" 2016-01-31 2099-12-31
share/db/concepts_candidates_2_exposure.csv view on Meta::CPAN
4316861 Accident caused by exposure to noise Observation SNOMED Event S "218226008" 2002-01-31 2099-12-31
4317932 Overexposure to sun rays Observation SNOMED Event S "218201004" 2002-01-31 2099-12-31
4317934 Overexposure to radioactive isotopes Observation SNOMED Event S "218209002" 2002-01-31 2099-12-31
4317935 Overexposure to radiobiologicals Observation SNOMED Event S "218210007" 2002-01-31 2099-12-31
4320000 Overexposure to microwave radiation Observation SNOMED Event S "218192005" 2002-01-31 2099-12-31
4320003 Overexposure to gamma rays Observation SNOMED Event S "218204007" 2002-01-31 2099-12-31
4320004 Overexposure to hard X-rays Observation SNOMED Event S "218205008" 2002-01-31 2099-12-31
4320005 Overexposure to soft X-rays Observation SNOMED Event S "218206009" 2002-01-31 2099-12-31
4320027 Exposure to extreme temperature, non-occupational Observation SNOMED Event S "95866005" 2002-01-31 2099-12-31
35622979 Occupational exposure to extreme temperature Observation SNOMED Event S "765226004" 2018-07-31 2099-12-31
37310260 Close exposure to SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) infection Observation SNOMED Event S "1240441000000108" 2020-02-04 2099-12-31
42535209 Occupational exposure to radiation Observation SNOMED Event S "16090451000119101" 2018-01-31 2099-12-31
42535211 Occupational exposure to toxic agents Observation SNOMED Event S "16090571000119109" 2018-01-31 2099-12-31
42535212 Occupational exposure to risk factor Observation SNOMED Event S "16090731000119102" 2018-01-31 2099-12-31
42535213 Occupational exposure to environmental tobacco smoke Observation SNOMED Event S "16090771000119104" 2018-01-31 2099-12-31
42536905 Occupational exposure to vibration Observation SNOMED Event S "735932007" 2018-01-31 2099-12-31
42539211 Occupational exposure to dust Observation SNOMED Event S "16090691000119109" 2018-01-31 2099-12-31
42539703 Occupational exposure to ergonomic risk Observation SNOMED Event S "737348000" 2018-01-31 2099-12-31
44790569 Accident due to water exposure Observation SNOMED Event S "240911000000102" 2006-10-02 2099-12-31
4072805 Accidental exposure to bipyridium compound herbicide Observation SNOMED Event S "242279004" 2002-01-31 2099-12-31
434543 Overexposure to visual and ultraviolet light sources Observation SNOMED Event S "218196008" 2002-01-31 2099-12-31
share/db/concepts_candidates_2_exposure.csv view on Meta::CPAN
438321 Accident due to exposure to weather conditions Observation SNOMED Event S "242575009" 2002-01-31 2099-12-31
438327 Overdose of radiation in therapy Observation SNOMED Event S "216958003" 2002-01-31 2099-12-31
438630 Exposure to radiation Observation SNOMED Event S "218190002" 2002-01-31 2099-12-31
439220 Overexposure to radiofrequency radiation Observation SNOMED Event S "218191003" 2002-01-31 2099-12-31
440608 Overexposure to infrared heater or lamp Observation SNOMED Event S "218195007" 2002-01-31 2099-12-31
442042 Exposure to radiation from diagnostic isotopes Observation SNOMED Event S "242811002" 2002-01-31 2099-12-31
443065 Accidental exposure to metals or their compounds Observation SNOMED Event S "242373001" 2002-01-31 2099-12-31
444046 Cold exposure Observation SNOMED Event S "40537000" 2002-01-31 2099-12-31
444128 Exposure to ionizing radiation Observation SNOMED Event S "122866006" 2002-01-31 2099-12-31
604443 Occupational exposure to SARS-CoV-2 Observation SNOMED Event S "897036007" 2021-01-31 2099-12-31
756064 Suspected exposure (but ruled out after evaluation) to Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Observation OMOP Extension Event S OMOP4873946 2020-03-18 2099-12-31
756083 Suspected exposure to Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Observation OMOP Extension Event S OMOP4873962 2020-03-18 2099-12-31
4008044 Exposure to polluted water, occupational Observation SNOMED Event S "102428006" 2002-01-31 2099-12-31
4008045 Exposure to polluted water, non-occupational Observation SNOMED Event S "102429003" 2002-01-31 2099-12-31
4008150 Exposure to toxic waste, occupational Observation SNOMED Event S "102439009" 2002-01-31 2099-12-31
4008152 Exposure to toxic dust, non-occupational Observation SNOMED Event S "102446000" 2002-01-31 2099-12-31
4009857 Exposure to environmental pollution, non-occupational Observation SNOMED Event S "102423002" 2002-01-31 2099-12-31
4009858 Exposure to polluted air, occupational Observation SNOMED Event S "102425009" 2002-01-31 2099-12-31
4009863 Exposure to toxic waste, non-occupational Observation SNOMED Event S "102440006" 2002-01-31 2099-12-31
4010326 Exposure to environmental pollution Observation SNOMED Event S "102421000" 2002-01-31 2099-12-31
4010327 Exposure to polluted air, non-occupational Observation SNOMED Event S "102426005" 2002-01-31 2099-12-31
4010328 Exposure to polluted soil, occupational Observation SNOMED Event S "102433005" 2002-01-31 2099-12-31
t/01-api-bff-pxf.t view on Meta::CPAN
my $got = $convert->bff2pxf;
$got->{$_} = undef for qw(id metaData);
is_deeply( $got, $pxf, 'bff2pxf module conversion matches fixture' );
}
{
my $gender = load_json_file('t/openehr2bff/in/gecco_personendaten.json');
my $ips = load_json_file('t/openehr2bff/in/ips_canonical.json');
my $lab = load_json_file('t/openehr2bff/in/laboratory_report.json');
my $corona = load_json_file('t/openehr2bff/in/compo_corona.json');
my $convert = build_convert(
method => 'openehr2pxf',
data => {
patient => { id => 'openehr-patient-2' },
compositions => [ $gender, $ips, $lab, $corona ],
},
in_textfile => 0,
);
my $tmp_file = temp_output_file( suffix => '.json' );
write_json_file( $tmp_file, $convert->openehr2pxf );
ok(
structured_files_match( 't/openehr2pxf/out/pxf.json', $tmp_file ),
'openehr2pxf module conversion matches fixture'
);
t/19-cli-regression.t view on Meta::CPAN
my $tmp_file = temp_output_file( suffix => '.json', dir => $tmpdir );
my $input_file = temp_output_file( suffix => '.json', dir => $tmpdir );
my $payload = {
patient => { id => 'openehr-patient-2' },
compositions => [
load_json_file('t/openehr2bff/in/gecco_personendaten.json'),
load_json_file('t/openehr2bff/in/ips_canonical.json'),
load_json_file('t/openehr2bff/in/laboratory_report.json'),
load_json_file('t/openehr2bff/in/compo_corona.json'),
],
};
write_json_file( $input_file, $payload );
my @cmd = ( $^X, $cli, '-iopenehr', $input_file, '-opxf', $tmp_file, '-O', '--test' );
my ( $exit, $output ) = run_cli(@cmd);
is( $exit, 0, 'CLI openehr2pxf exits successfully' )
or diag $output;
ok(
t/21-openehr-behavior.t view on Meta::CPAN
build_convert
load_json_file
temp_output_file
write_json_file
structured_files_match
);
my $gender = load_json_file('t/openehr2bff/in/gecco_personendaten.json');
my $ips = load_json_file('t/openehr2bff/in/ips_canonical.json');
my $lab = load_json_file('t/openehr2bff/in/laboratory_report.json');
my $corona = load_json_file('t/openehr2bff/in/compo_corona.json');
sub with_subject_id {
my ( $composition, $id ) = @_;
my %copy = %{$composition};
$copy{subject} = {
_type => 'PARTY_SELF',
external_ref => {
id => { _type => 'GENERIC_ID', value => $id, scheme => 'PMI' },
namespace => 'PMI',
type => 'PERSON',
t/21-openehr-behavior.t view on Meta::CPAN
is( $individual->{id}, 'openehr-patient-1', 'uses patient id from the envelope' );
is( $individual->{sex}{id}, 'NCIT:C20197', 'maps administrative gender to Beacon sex term' );
is( scalar @{ $individual->{info}{openehr}{compositions} }, 2, 'preserves all source compositions under info.openehr' );
};
subtest 'openehr2bff emits first-class arrays from multiple canonical compositions' => sub {
my $convert = build_convert(
method => 'openehr2bff',
data => {
patient => { id => 'openehr-patient-2' },
compositions => [ $gender, $ips, $lab, $corona ],
},
in_textfile => 0,
);
my $individual = $convert->openehr2bff;
is( scalar @{ $individual->{diseases} }, 3, 'maps problem diagnosis entries to diseases' );
is( scalar @{ $individual->{measures} }, 2, 'maps multiple observations with values to measures' );
is( scalar @{ $individual->{phenotypicFeatures} }, 7, 'maps symptom screening observations to phenotypicFeatures' );
is( scalar @{ $individual->{interventionsOrProcedures} }, 1, 'maps procedure actions to interventionsOrProcedures' );
t/omop2bff/out/individuals.json view on Meta::CPAN
"iso8601duration" : "P51Y"
}
},
"bodySite" : {
"id" : "NCIT:C126101",
"label" : "Not Available"
},
"dateOfProcedure" : "2012-06-06",
"procedureCode" : {
"id" : "SNOMED:415070008",
"label" : "Percutaneous coronary intervention"
}
},
{
"_info" : {
"PROCEDURE_OCCURRENCE" : {
"OMOP_columns" : {
"modifier_concept_id" : 0,
"modifier_source_value" : null,
"person_id" : 662,
"procedure_concept_id" : 4336464,
t/omop2bff/out/individuals.json view on Meta::CPAN
"iso8601duration" : "P56Y"
}
},
"bodySite" : {
"id" : "NCIT:C126101",
"label" : "Not Available"
},
"dateOfProcedure" : "2005-08-28",
"procedureCode" : {
"id" : "SNOMED:415070008",
"label" : "Percutaneous coronary intervention"
}
},
{
"_info" : {
"PROCEDURE_OCCURRENCE" : {
"OMOP_columns" : {
"modifier_concept_id" : 0,
"modifier_source_value" : null,
"person_id" : 709,
"procedure_concept_id" : 4151422,
t/omop2pxf/out/pxf.json view on Meta::CPAN
"id" : null,
"medicalActions" : [
{
"procedure" : {
"bodySite" : {
"id" : "NCIT:C126101",
"label" : "Not Available"
},
"code" : {
"id" : "SNOMED:415070008",
"label" : "Percutaneous coronary intervention"
},
"performed" : {
"age" : {
"iso8601duration" : "P51Y"
}
}
}
},
{
"procedure" : {
t/omop2pxf/out/pxf.json view on Meta::CPAN
}
},
{
"procedure" : {
"bodySite" : {
"id" : "NCIT:C126101",
"label" : "Not Available"
},
"code" : {
"id" : "SNOMED:415070008",
"label" : "Percutaneous coronary intervention"
},
"performed" : {
"age" : {
"iso8601duration" : "P56Y"
}
}
}
},
{
"procedure" : {
t/openehr2bff/in/README.md view on Meta::CPAN
- repository: <https://github.com/ehrbase/openEHR_SDK>
- source directory:
`test-data/src/main/resources/composition/canonical_json/`
Copied files:
- `ips_canonical.json`
- `laboratory_report.json`
- `gecco_personendaten.json`
- `compo_corona.json`
Derived local fixture:
- `gecco_personendaten_patient.json`
Derived from `gecco_personendaten.json` by adding
`subject.external_ref.id.value = openehr-patient-2`
for patient-identified openEHR input tests.
## Note
( run in 2.894 seconds using v1.01-cache-2.11-cpan-39bf76dae61 )