OBSERVATION-from-assessments
============================

*Source file:* ``OBSERVATION-from-assessments.py``

Root XPath
----------

.. code-block:: xpath

    ./hl7:component/hl7:structuredBody/hl7:component/hl7:section/hl7:templateId[ @root="2.16.840.1.113883.10.20.22.2.8" or @root="2.16.840.1.113883.10.20.22.2.8.1"]/..

**Expected OMOP domain:** Observation

Fields
------

+------------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Field                              | Type     | Order | Details                                                                                                                                                                                                                                                         |
+====================================+==========+=======+=================================================================================================================================================================================================================================================================+
| observation_id                     | HASH     | 1     | hash(person_id, provider_id, observation_concept_code, observation_concept_codeSystem, observation_date, value_as_string, unit_source_value)                                                                                                                    |
+------------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| person_id                          | FK       | 2     | FK → ``person_id``                                                                                                                                                                                                                                              |
+------------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| observation_concept_id             | DERIVED  | 3     | ``VT.codemap_xwalk_concept_id(concept_code=observation_concept_code, vocabulary_oid=observation_concept_codeSystem)``                                                                                                                                           |
+------------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| observation_date                   | FIELD    | 4     | ``hl7:effectiveTime`` @value [DATE]                                                                                                                                                                                                                             |
+------------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| observation_datetime               | PRIORITY | 5     | coalesce candidates by priority                                                                                                                                                                                                                                 |
+------------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| observation_type_concept_id        | CONSTANT | 6     | ``32827``                                                                                                                                                                                                                                                       |
+------------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| value_as_number                    | FIELD    | 7     | ``hl7:value[@xsi:type="PQ"]`` @value [FLOAT]                                                                                                                                                                                                                    |
+------------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| value_as_string                    | DERIVED  | 8     | ``VT.concat_fields(first_field=title_value, second_field=text_value)``                                                                                                                                                                                          |
+------------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| value_as_concept_id                | DERIVED  | 9     | ``VT.codemap_xwalk_concept_id(concept_code=value_code, vocabulary_oid=value_codeSystem)``                                                                                                                                                                       |
+------------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| qualifier_concept_id               | None     | 10    | —                                                                                                                                                                                                                                                               |
+------------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| unit_concept_id                    | DERIVED  | 11    | ``VT.codemap_xwalk_concept_id(concept_code=unit_source_value, vocabulary_oid=unit_codeSystem)``                                                                                                                                                                 |
+------------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| provider_id                        | None     | 12    | —                                                                                                                                                                                                                                                               |
+------------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| visit_occurrence_id                | FK       | 13    | FK → ``visit_occurrence_id``                                                                                                                                                                                                                                    |
+------------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| visit_detail_id                    | None     | 14    | —                                                                                                                                                                                                                                                               |
+------------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| observation_source_value           | DERIVED2 | 15    | {'config_type': 'DERIVED2', 'FUNCTION': VT.concat_field_list_values, 'argument_list': {'key_list': ['observation_concept_code', 'observation_concept_codeSystem', 'value_codeSystem', 'value_code', 'value_as_string', 'value_as_number_string']}, 'order': 15} |
+------------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| observation_source_concept_id      | DERIVED  | 16    | ``VT.codemap_xwalk_source_concept_id(concept_code=observation_concept_code, vocabulary_oid=observation_concept_codeSystem)``                                                                                                                                    |
+------------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| unit_source_value                  | FIELD    | 17    | ``hl7:value`` @unit                                                                                                                                                                                                                                             |
+------------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| qualifier_source_value             | CONSTANT | 18    | ````                                                                                                                                                                                                                                                            |
+------------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| data_partner_id                    | DERIVED  | 20    | ``VT.get_data_partner_id(filename=filename)``                                                                                                                                                                                                                   |
+------------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| filename                           | FILENAME | 100   | source XML filename                                                                                                                                                                                                                                             |
+------------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| cfg_name                           | CONSTANT | 101   | ``OBSERVATION-from-assessments``                                                                                                                                                                                                                                |
+------------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| domain_id                          | DERIVED  |       | ``VT.codemap_xwalk_domain_id(concept_code=observation_concept_code, vocabulary_oid=observation_concept_codeSystem)``                                                                                                                                            |
+------------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| observation_concept_code           | FIELD    |       | ``hl7:code`` @code                                                                                                                                                                                                                                              |
+------------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| observation_concept_codeSystem     | FIELD    |       | ``hl7:code`` @codeSystem                                                                                                                                                                                                                                        |
+------------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| observation_datetime_effectiveTime | FIELD    |       | ``hl7:effectiveTime`` @value [DATETIME_LOW] → priority ['observation_datetime', 1]                                                                                                                                                                              |
+------------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| observation_datetime_high          | FIELD    |       | ``hl7:effectiveTime/hl7:high`` @value [DATETIME_HIGH] → priority ['observation_datetime', 3]                                                                                                                                                                    |
+------------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| observation_datetime_low           | FIELD    |       | ``hl7:effectiveTime/hl7:low`` @value [DATETIME_LOW] → priority ['observation_datetime', 2]                                                                                                                                                                      |
+------------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| text_value                         | FIELD    |       | ``hl7:text`` @value [TEXT]                                                                                                                                                                                                                                      |
+------------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| title_value                        | FIELD    |       | ``hl7:title`` @value [TEXT]                                                                                                                                                                                                                                     |
+------------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| unit_codeSystem                    | CONSTANT |       | ``2.16.840.1.113883.6.8``                                                                                                                                                                                                                                       |
+------------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| value_as_number_string             | FIELD    |       | ``hl7:value`` @value                                                                                                                                                                                                                                            |
+------------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| value_code                         | FIELD    |       | ``hl7:value`` @code                                                                                                                                                                                                                                             |
+------------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| value_codeSystem                   | FIELD    |       | ``hl7:value`` @codeSystem                                                                                                                                                                                                                                       |
+------------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+

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)                                    |
+-------------+----------------------------------------------------------------+