MEASUREMENT-from-vital_signs_organizer_observation ================================================== *Source file:* ``MEASUREMENT-from-vital_signs_organizer_observation.py`` Root XPath ---------- .. code-block:: xpath ./hl7:component/hl7:structuredBody/hl7:component/hl7:section/hl7:templateId[@root='2.16.840.1.113883.10.20.22.2.4' or @root='2.16.840.1.113883.10.20.22.2.4.1']/../hl7:entry/hl7:organizer/hl7:component/hl7:observation **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-vital_signs_organizer_observation`` | +--------------------------------+----------+-------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ | 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) | +-------------+----------------------------------------------------------------+