PROCEDURE-from-procedure_observation
====================================

*Source file:* ``PROCEDURE-from-procedure_observation.py``

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

.. code-block:: xpath

    ./hl7:component/hl7:structuredBody/hl7:component/hl7:section/hl7:templateId[@root='2.16.840.1.113883.10.20.22.2.7' or @root='2.16.840.1.113883.10.20.22.2.7.1']/../hl7:entry/hl7:observation[@moodCode='EVN']/hl7:statusCode[@code='active' or @code='completed']/..

**Expected OMOP domain:** Procedure

Fields
------

+-----------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Field                             | Type     | Order | Details                                                                                                                                                                                 |
+===================================+==========+=======+=========================================================================================================================================================================================+
| procedure_occurrence_id           | HASH     | 1     | hash(person_id, provider_id, procedure_concept_code, procedure_concept_codeSystem, procedure_date, procedure_datetime, procedure_occurrence_id_root, procedure_occurrence_id_extension) |
+-----------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| person_id                         | FK       | 2     | FK → ``person_id``                                                                                                                                                                      |
+-----------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| procedure_concept_id              | DERIVED  | 3     | ``VT.codemap_xwalk_concept_id(concept_code=procedure_concept_code, vocabulary_oid=procedure_concept_codeSystem)``                                                                       |
+-----------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| procedure_date                    | PRIORITY | 4     | coalesce candidates by priority                                                                                                                                                         |
+-----------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| procedure_datetime                | PRIORITY | 5     | coalesce candidates by priority                                                                                                                                                         |
+-----------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| procedure_type_concept_id         | CONSTANT | 6     | ``32817``                                                                                                                                                                               |
+-----------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| modifier_concept_id               | None     | 7     | —                                                                                                                                                                                       |
+-----------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| quantity                          | None     | 8     | —                                                                                                                                                                                       |
+-----------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| provider_id                       | FK       | 9     | FK → ``provider_id``                                                                                                                                                                    |
+-----------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| visit_occurrence_id               | FK       | 10    | FK → ``visit_occurrence_id``                                                                                                                                                            |
+-----------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| visit_detail_id                   | None     | 11    | —                                                                                                                                                                                       |
+-----------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| procedure_source_value            | DERIVED  | 12    | ``VT.concat_fields(first_field=procedure_concept_code, second_field=procedure_concept_codeSystem)``                                                                                     |
+-----------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| procedure_source_concept_id       | DERIVED  | 13    | ``VT.codemap_xwalk_source_concept_id(concept_code=procedure_concept_code, vocabulary_oid=procedure_concept_codeSystem)``                                                                |
+-----------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| modifier_source_value             | CONSTANT | 14    | ````                                                                                                                                                                                    |
+-----------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| data_partner_id                   | DERIVED  | 20    | ``VT.get_data_partner_id(filename=filename)``                                                                                                                                           |
+-----------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| filename                          | FILENAME | 100   | source XML filename                                                                                                                                                                     |
+-----------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| cfg_name                          | CONSTANT | 101   | ``PROCEDURE-from-procedure_observation``                                                                                                                                                |
+-----------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| domain_id                         | DERIVED  |       | ``VT.codemap_xwalk_domain_id(concept_code=procedure_concept_code, vocabulary_oid=procedure_concept_codeSystem)``                                                                        |
+-----------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| procedure_concept_code            | FIELD    |       | ``hl7:code`` @code                                                                                                                                                                      |
+-----------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| procedure_concept_codeSystem      | FIELD    |       | ``hl7:code`` @codeSystem                                                                                                                                                                |
+-----------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| procedure_date_eT                 | FIELD    |       | ``hl7:effectiveTime`` @value [DATE] → priority ['procedure_date', 1]                                                                                                                    |
+-----------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| procedure_date_high               | FIELD    |       | ``hl7:effectiveTime/hl7:high`` @value [DATE] → priority ['procedure_date', 3]                                                                                                           |
+-----------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| procedure_date_low                | FIELD    |       | ``hl7:effectiveTime/hl7:low`` @value [DATE] → priority ['procedure_date', 2]                                                                                                            |
+-----------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| procedure_datetime_eT             | FIELD    |       | ``hl7:effectiveTime`` @value [DATETIME] → priority ['procedure_datetime', 1]                                                                                                            |
+-----------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| procedure_datetime_high           | FIELD    |       | ``hl7:effectiveTime/hl7:high`` @value [DATETIME] → priority ['procedure_datetime', 3]                                                                                                   |
+-----------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| procedure_datetime_low            | FIELD    |       | ``hl7:effectiveTime/hl7:low`` @value [DATETIME] → priority ['procedure_datetime', 2]                                                                                                    |
+-----------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| procedure_occurrence_id_extension | FIELD    |       | ``hl7:id[not(@nullFlavor="UNK")]`` @extension                                                                                                                                           |
+-----------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| procedure_occurrence_id_root      | FIELD    |       | ``hl7:id[not(@nullFlavor="UNK")]`` @root                                                                                                                                                |
+-----------------------------------+----------+-------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+

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