MEASUREMENT-from-results_procedure

Source file: MEASUREMENT-from-results_procedure.py

Root XPath

./hl7:component/hl7:structuredBody/hl7:component/hl7:section/hl7:templateId[@root='2.16.840.1.113883.10.20.22.2.3' or @root='2.16.840.1.113883.10.20.22.2.3.1']/../hl7:entry/hl7:organizer/hl7:component/hl7:procedure

Expected OMOP domain: Measurement

Fields

Field

Type

Order

Details

measurement_id

HASH

1

hash(person_id, provider_id, measurement_concept_code, measurement_concept_codeSystem, measurement_date, measurement_datetime, value_as_number, value_as_concept_id, measurement_id_root, measurement_id_extension, value_source_value, unit_source_value)

person_id

FK

2

FK → person_id

measurement_concept_id

DERIVED

3

VT.codemap_xwalk_concept_id(concept_code=measurement_concept_code, vocabulary_oid=measurement_concept_codeSystem)

measurement_date

PRIORITY

4

coalesce candidates by priority

measurement_datetime

PRIORITY

5

coalesce candidates by priority

measurement_time

CONSTANT

6

measurement_type_concept_id

CONSTANT

7

32827

operator_concept_id

CONSTANT

8

0

value_as_number

PRIORITY

9

coalesce candidates by priority

value_as_concept_id

PRIORITY

10

coalesce candidates by priority

unit_concept_id

DERIVED

11

VT.codemap_xwalk_concept_id(concept_code=unit_source_value, vocabulary_oid=unit_codeSystem)

range_low

None

12

—

range_high

None

13

—

provider_id

None

14

—

visit_occurrence_id

FK

15

FK → visit_occurrence_id

visit_detail_id

None

16

—

measurement_source_value

DERIVED

17

VT.concat_fields(first_field=measurement_concept_code, second_field=measurement_concept_codeSystem)

measurement_source_concept_id

DERIVED

18

VT.codemap_xwalk_source_concept_id(concept_code=measurement_concept_code, vocabulary_oid=measurement_concept_codeSystem)

unit_source_value

FIELD

19

hl7:value @unit

value_source_value

DERIVED2

20

{‘config_type’: ‘DERIVED2’, ‘FUNCTION’: VT.concat_field_list_values, ‘argument_list’: {‘key_list’: [‘value_as_codeSystem_CE’, ‘value_as_code_CE’, ‘value_as_codeSystem_CD’, ‘value_as_code_CD’, ‘value_as_codeSystem_XX’, ‘value_as_code_XX’, ‘value_source_value_quantity’, ‘value_source_value_text’]}, ‘order’: 20}

data_partner_id

DERIVED

24

VT.get_data_partner_id(filename=filename)

filename

FILENAME

100

source XML filename

cfg_name

CONSTANT

101

MEASUREMENT-from-results_procedure

domain_id

DERIVED

VT.codemap_xwalk_domain_id(concept_code=measurement_concept_code, vocabulary_oid=measurement_concept_codeSystem)

measurement_concept_code

FIELD

hl7:code @code

measurement_concept_codeSystem

FIELD

hl7:code @codeSystem

measurement_date_eT

FIELD

hl7:effectiveTime @value [DATE] → priority [‘measurement_date’, 1]

measurement_date_high

FIELD

hl7:effectiveTime/hl7:high @value [DATE] → priority [‘measurement_date’, 3]

measurement_date_low

FIELD

hl7:effectiveTime/hl7:low @value [DATE] → priority [‘measurement_date’, 2]

measurement_datetime_eT

FIELD

hl7:effectiveTime @value [DATETIME] → priority [‘measurement_datetime’, 1]

measurement_datetime_high

FIELD

hl7:effectiveTime/hl7:high @value [DATETIME] → priority [‘measurement_datetime’, 3]

measurement_datetime_low

FIELD

hl7:effectiveTime/hl7:low @value [DATETIME] → priority [‘measurement_datetime’, 2]

measurement_id_extension

FIELD

hl7:id[not(@nullFlavor="UNK")] @extension

measurement_id_root

FIELD

hl7:id[not(@nullFlavor="UNK")] @root

unit_codeSystem

CONSTANT

2.16.840.1.113883.6.8

value_as_codeSystem_CD

FIELD

hl7:value[@xsi:type="CD"] @codeSystem

value_as_codeSystem_CE

FIELD

hl7:value[@xsi:type="CE"] @codeSystem

value_as_codeSystem_XX

FIELD

hl7:value @codeSystem

value_as_code_CD

FIELD

hl7:value[@xsi:type="CD"] @code

value_as_code_CE

FIELD

hl7:value[@xsi:type="CE"] @code

value_as_code_XX

FIELD

hl7:value @code

value_as_concept_id_CD

DERIVED

VT.codemap_xwalk_concept_id(concept_code=value_as_code_CD, vocabulary_oid=value_as_codeSystem_CD)

value_as_concept_id_CE

DERIVED

VT.codemap_xwalk_concept_id(concept_code=value_as_code_CE, vocabulary_oid=value_as_codeSystem_CE)

value_as_concept_id_XX

DERIVED

VT.codemap_xwalk_concept_id(concept_code=value_as_code_XX, vocabulary_oid=value_as_codeSystem_XX)

value_as_number_pq

FIELD

hl7:value[@xsi:type="PQ"] @value [FLOAT] → priority [‘value_as_number’, 1]

value_source_value_quantity

FIELD

hl7:value @value

value_source_value_text

FIELD

hl7:value @#text

value_type

FIELD

hl7:value @{http://www.w3.org/2001/XMLSchema-instance}type

Config type reference

config_type

Meaning

ROOT

Defines the XPath root element for this config

FIELD

Extracts an XML attribute value via XPath

DERIVED

Computed by a Python function from other fields

HASH

MD5/hash of a set of fields, used as a surrogate key

FK

Foreign key copied from a joined dataset

CONSTANT

Fixed literal value written to every row

PRIORITY

Coalesces the first non-null value from prioritized candidates

FILENAME

The source XML filename

None

Not populated (placeholder)