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<header>
<h1 class="title">Module <code>Gnumed.business.gmLOINC</code></h1>
</header>
<section id="section-intro">
<p>LOINC handling code.</p>
<p><a href="http://loinc.org">http://loinc.org</a></p>
<p>license: GPL v2 or later</p>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python"># -*- coding: utf-8 -*-
&#34;&#34;&#34;LOINC handling code.

http://loinc.org

license: GPL v2 or later
&#34;&#34;&#34;
#============================================================
__author__ = &#34;K.Hilbert &lt;Karsten.Hilbert@gmx.net&gt;&#34;

import sys
import logging
import csv
import re as regex


if __name__ == &#39;__main__&#39;:
        sys.path.insert(0, &#39;../../&#39;)
from Gnumed.pycommon import gmPG2
from Gnumed.pycommon import gmTools
from Gnumed.pycommon import gmMatchProvider


_log = logging.getLogger(&#39;gm.loinc&#39;)


origin_url = &#39;http://loinc.org&#39;
file_encoding = &#39;latin1&#39;                        # encoding is empirical
license_delimiter = &#39;Clip Here for Data&#39;
version_tag = &#39;LOINC(R) Database Version&#39;
name_long = &#39;LOINC® (Logical Observation Identifiers Names and Codes)&#39;
name_short = &#39;LOINC&#39;

loinc_fields = &#34;LOINC_NUM COMPONENT PROPERTY TIME_ASPCT SYSTEM SCALE_TYP METHOD_TYP RELAT_NMS CLASS SOURCE DT_LAST_CH CHNG_TYPE COMMENTS ANSWERLIST STATUS MAP_TO SCOPE NORM_RANGE IPCC_UNITS REFERENCE EXACT_CMP_SY MOLAR_MASS CLASSTYPE FORMULA SPECIES EXMPL_ANSWERS ACSSYM BASE_NAME FINAL NAACCR_ID CODE_TABLE SETROOT PANELELEMENTS SURVEY_QUEST_TEXT SURVEY_QUEST_SRC UNITSREQUIRED SUBMITTED_UNITS RELATEDNAMES2 SHORTNAME ORDER_OBS CDISC_COMMON_TESTS HL7_FIELD_SUBFIELD_ID EXTERNAL_COPYRIGHT_NOTICE EXAMPLE_UNITS INPC_PERCENTAGE LONG_COMMON_NAME&#34;.split()

#============================================================

LOINC_creatinine_quantity = [&#39;2160-0&#39;, &#39;14682-9&#39;, &#39;40264-4&#39;, &#39;40248-7&#39;]
LOINC_gfr_quantity = [&#39;33914-3&#39;, &#39;45066-8&#39;, &#39;48642-3&#39;, &#39;48643-1&#39;, &#39;50044-7&#39;, &#39;50210-4&#39;, &#39;50384-7&#39;, &#39;62238-1&#39;, &#39;69405-9&#39;, &#39;70969-1&#39;]
LOINC_height = [&#39;3137-7&#39;, &#39;3138-5&#39;, &#39;8301-4&#39;, &#39;8302-2&#39;, &#39;8305-5&#39;, &#39;8306-3&#39;, &#39;8307-1&#39;, &#39;8308-9&#39;]
LOINC_weight = [&#39;18833-4&#39;, &#39;29463-7&#39;, &#39;3141-9&#39;, &#39;3142-7&#39;, &#39;8335-2&#39;, &#39;8339-4&#39;, &#39;8344-4&#39;, &#39;8346-9&#39;, &#39;8351-9&#39;]
LOINC_rr_quantity = [&#39;8478-0&#39;, &#39;8448-3&#39;, &#39;8449-1&#39;, &#39;8456-6&#39;, &#39;8457-4&#39;, &#39;8458-2&#39;, &#39;55284-4&#39;, &#39;50403-5&#39;, &#39;50402-7&#39;, &#39;45372-0&#39;]
LOINC_heart_rate_quantity = [&#39;8867-4&#39;, &#39;67129-7&#39;, &#39;40443-4&#39;, &#39;69000-8&#39;, &#39;69001-6&#39;, &#39;68999-2&#39;]
LOINC_inr_quantity = [&#39;34714-6&#39;, &#39;46418-0&#39;, &#39;6301-6&#39;, &#39;38875-1&#39;]

#============================================================
# convenience functions
#------------------------------------------------------------
def format_loinc(loinc):
        data = loinc2data(loinc)
        if data is None:
                return None
        return gmTools.format_dict_like (
                dict(data),
                tabular = True,
                value_delimiters = None,
                values2ignore = [None, &#39;&#39;]
        )

#------------------------------------------------------------
def loinc2data(loinc):
        cmd = &#39;SELECT * FROM ref.loinc WHERE code = %(loinc)s&#39;
        args = {&#39;loinc&#39;: loinc}
        rows = gmPG2.run_ro_queries(queries = [{&#39;cmd&#39;: cmd, &#39;args&#39;: args}])
        if len(rows) == 0:
                return None
        return rows[0]

#------------------------------------------------------------
def loinc2term(loinc=None):

        # NOTE: will return [NULL] on no-match due to the coalesce()
        cmd = &#34;&#34;&#34;
SELECT coalesce (
        (SELECT term
        FROM ref.v_coded_terms
        WHERE
                coding_system = &#39;LOINC&#39;
                        AND
                code = %(loinc)s
                        AND
                lang = i18n.get_curr_lang()
        ),
        (SELECT term
        FROM ref.v_coded_terms
        WHERE
                coding_system = &#39;LOINC&#39;
                        AND
                code = %(loinc)s
                        AND
                lang = &#39;en_EN&#39;
        ),
        (SELECT term
        FROM ref.v_coded_terms
        WHERE
                coding_system = &#39;LOINC&#39;
                        AND
                code = %(loinc)s
        )
)&#34;&#34;&#34;
        args = {&#39;loinc&#39;: loinc}
        rows = gmPG2.run_ro_queries(queries = [{&#39;cmd&#39;: cmd, &#39;args&#39;: args}])

        if rows[0][0] is None:
                return []

        return [ r[0] for r in rows ]

#============================================================
# LOINCDBTXT handling
#------------------------------------------------------------
def split_LOINCDBTXT(input_fname=None, data_fname=None, license_fname=None):

        _log.debug(&#39;splitting LOINC source file [%s]&#39;, input_fname)

        if license_fname is None:
                license_fname = gmTools.get_unique_filename(prefix = &#39;loinc_license-&#39;, suffix = &#39;.txt&#39;)
        _log.debug(&#39;LOINC header: %s&#39;, license_fname)

        if data_fname is None:
                data_fname = gmTools.get_unique_filename(prefix = &#39;loinc_data-&#39;, suffix = &#39;.csv&#39;)
        _log.debug(&#39;LOINC data: %s&#39;, data_fname)

        loinc_file = open(input_fname, mode = &#39;rt&#39;, encoding = file_encoding, errors = &#39;replace&#39;)
        out_file = open(license_fname, mode = &#39;wt&#39;, encoding = &#39;utf8&#39;, errors = &#39;replace&#39;)

        for line in loinc_file:

                if license_delimiter in line:
                        out_file.write(line)
                        out_file.close()
                        out_file = open(data_fname, mode = &#39;wt&#39;, encoding = &#39;utf8&#39;, errors = &#39;replace&#39;)
                        continue

                out_file.write(line)

        out_file.close()

        return data_fname, license_fname

#============================================================
def map_field_names(data_fname=&#39;loinc_data.csv&#39;):

        csv_file = open(data_fname, mode = &#39;rt&#39;, encoding = &#39;utf-8-sig&#39;, errors = &#39;replace&#39;)
        first_line = csv_file.readline()
        sniffer = csv.Sniffer()
        if sniffer.has_header(first_line):
                pass

#============================================================
def get_version(license_fname=&#39;loinc_license.txt&#39;):

        in_file = open(license_fname, mode = &#39;rt&#39;, encoding = &#39;utf-8-sig&#39;, errors = &#39;replace&#39;)

        version = None
        for line in in_file:
                if line.startswith(version_tag):
                        version = line[len(version_tag):].strip()
                        break

        in_file.close()
        return version

#============================================================
def loinc_import(data_fname=None, license_fname=None, version=None, conn=None, lang=&#39;en_EN&#39;):

        if version is None:
                version = get_version(license_fname = license_fname)

        if version is None:
                raise ValueError(&#39;cannot detect LOINC version&#39;)

        _log.debug(&#39;importing LOINC version [%s]&#39;, version)

        # clean out staging area
        curs = conn.cursor()
        cmd = &#34;&#34;&#34;DELETE FROM staging.loinc_staging&#34;&#34;&#34;
        gmPG2.run_rw_queries(link_obj = curs, queries = [{&#39;cmd&#39;: cmd}])
        curs.close()
        conn.commit()
        _log.debug(&#39;staging table emptied&#39;)

        # import data from csv file into staging table
        csv_file = open(data_fname, mode = &#39;rt&#39;, encoding = &#39;utf-8-sig&#39;, errors = &#39;replace&#39;)
        loinc_reader = gmTools.unicode_csv_reader(csv_file, delimiter = &#34;\t&#34;, quotechar = &#39;&#34;&#39;)
        curs = conn.cursor()
        cmd = &#34;&#34;&#34;INSERT INTO staging.loinc_staging values (%s%%s)&#34;&#34;&#34; % (&#39;%s, &#39; * (len(loinc_fields) - 1))
        first = False
        for loinc_line in loinc_reader:
                if not first:
                        first = True
                        continue
                gmPG2.run_rw_queries(link_obj = curs, queries = [{&#39;cmd&#39;: cmd, &#39;args&#39;: loinc_line}])
        curs.close()
        conn.commit()
        csv_file.close()
        _log.debug(&#39;staging table loaded&#39;)

        # create data source record
        in_file = open(license_fname, mode = &#39;rt&#39;, encoding = &#39;utf-8-sig&#39;, errors = &#39;replace&#39;)
        desc = in_file.read()
        in_file.close()
        args = {&#39;ver&#39;: version, &#39;desc&#39;: desc, &#39;url&#39;: origin_url, &#39;name_long&#39;: name_long, &#39;name_short&#39;: name_short, &#39;lang&#39;: lang}
        queries = [
                # insert if not existing
                {&#39;args&#39;: args, &#39;cmd&#39;: &#34;&#34;&#34;
                        INSERT INTO ref.data_source (name_long, name_short, version) SELECT
                                %(name_long)s,
                                %(name_short)s,
                                %(ver)s
                        WHERE NOT EXISTS (
                                SELECT 1 FROM ref.data_source WHERE
                                        name_long = %(name_long)s
                                                AND
                                        name_short = %(name_short)s
                                                AND
                                        version = %(ver)s
                        )&#34;&#34;&#34;
                },
                # update non-unique fields
                {&#39;args&#39;: args, &#39;cmd&#39;: &#34;&#34;&#34;
                        UPDATE ref.data_source SET
                                description = %(desc)s,
                                source = %(url)s,
                                lang = %(lang)s
                        WHERE
                                name_long = %(name_long)s
                                        AND
                                name_short = %(name_short)s
                                        AND
                                version = %(ver)s
                        &#34;&#34;&#34;
                },
                # retrieve PK of data source
                {&#39;args&#39;: args, &#39;cmd&#39;: &#34;&#34;&#34;SELECT pk FROM ref.data_source WHERE name_short = %(name_short)s AND version = %(ver)s&#34;&#34;&#34;}
        ]
        curs = conn.cursor()
        rows = gmPG2.run_rw_queries(link_obj = curs, queries = queries, return_data = True)
        data_src_pk = rows[0][0]
        curs.close()
        _log.debug(&#39;data source record created or updated, pk is #%s&#39;, data_src_pk)

        # import from staging table to real table
        args = {&#39;src_pk&#39;: data_src_pk}
        queries = []
        queries.append ({
                &#39;args&#39;: args,
                &#39;cmd&#39;: &#34;&#34;&#34;
                        INSERT INTO ref.loinc (
                                fk_data_source, term, code
                        )
                        SELECT
                                %(src_pk)s,
                                coalesce (
                                        nullif(long_common_name, &#39;&#39;),
                                        (
                                                coalesce(nullif(component, &#39;&#39;) || &#39;:&#39;, &#39;&#39;) ||
                                                coalesce(nullif(property, &#39;&#39;) || &#39;:&#39;, &#39;&#39;) ||
                                                coalesce(nullif(time_aspect, &#39;&#39;) || &#39;:&#39;, &#39;&#39;) ||
                                                coalesce(nullif(system, &#39;&#39;) || &#39;:&#39;, &#39;&#39;) ||
                                                coalesce(nullif(scale_type, &#39;&#39;) || &#39;:&#39;, &#39;&#39;) ||
                                                coalesce(nullif(method_type, &#39;&#39;) || &#39;:&#39;, &#39;&#39;)
                                        )
                                ),
                                nullif(loinc_num, &#39;&#39;)
                        FROM
                                staging.loinc_staging st_ls
                        WHERE NOT EXISTS (
                                SELECT 1 FROM ref.loinc r_l WHERE
                                        r_l.fk_data_source = %(src_pk)s
                                                AND
                                        r_l.code = nullif(st_ls.loinc_num, &#39;&#39;)
                                                AND
                                        r_l.term =      coalesce (
                                                nullif(st_ls.long_common_name, &#39;&#39;),
                                                (
                                                        coalesce(nullif(st_ls.component, &#39;&#39;) || &#39;:&#39;, &#39;&#39;) ||
                                                        coalesce(nullif(st_ls.property, &#39;&#39;) || &#39;:&#39;, &#39;&#39;) ||
                                                        coalesce(nullif(st_ls.time_aspect, &#39;&#39;) || &#39;:&#39;, &#39;&#39;) ||
                                                        coalesce(nullif(st_ls.system, &#39;&#39;) || &#39;:&#39;, &#39;&#39;) ||
                                                        coalesce(nullif(st_ls.scale_type, &#39;&#39;) || &#39;:&#39;, &#39;&#39;) ||
                                                        coalesce(nullif(st_ls.method_type, &#39;&#39;) || &#39;:&#39;, &#39;&#39;)
                                                )
                                        )
                        )&#34;&#34;&#34;
        })
        queries.append ({
                &#39;args&#39;: args,
                &#39;cmd&#39;: &#34;&#34;&#34;
                        UPDATE ref.loinc SET
                                comment = nullif(st_ls.comments, &#39;&#39;),
                                component = nullif(st_ls.component, &#39;&#39;),
                                property = nullif(st_ls.property, &#39;&#39;),
                                time_aspect = nullif(st_ls.time_aspect, &#39;&#39;),
                                system = nullif(st_ls.system, &#39;&#39;),
                                scale_type = nullif(st_ls.scale_type, &#39;&#39;),
                                method_type = nullif(st_ls.method_type, &#39;&#39;),
                                related_names_1_old = nullif(st_ls.related_names_1_old, &#39;&#39;),
                                grouping_class = nullif(st_ls.class, &#39;&#39;),
                                loinc_internal_source = nullif(st_ls.source, &#39;&#39;),
                                dt_last_change = nullif(st_ls.dt_last_change, &#39;&#39;),
                                change_type = nullif(st_ls.change_type, &#39;&#39;),
                                answer_list = nullif(st_ls.answer_list, &#39;&#39;),
                                code_status = nullif(st_ls.status, &#39;&#39;),
                                maps_to = nullif(st_ls.map_to, &#39;&#39;),
                                scope = nullif(st_ls.scope, &#39;&#39;),
                                normal_range = nullif(st_ls.normal_range, &#39;&#39;),
                                ipcc_units = nullif(st_ls.ipcc_units, &#39;&#39;),
                                reference = nullif(st_ls.reference, &#39;&#39;),
                                exact_component_synonym = nullif(st_ls.exact_component_synonym, &#39;&#39;),
                                molar_mass = nullif(st_ls.molar_mass, &#39;&#39;),
                                grouping_class_type = nullif(st_ls.class_type, &#39;&#39;)::smallint,
                                formula = nullif(st_ls.formula, &#39;&#39;),
                                species = nullif(st_ls.species, &#39;&#39;),
                                example_answers = nullif(st_ls.example_answers, &#39;&#39;),
                                acs_synonyms = nullif(st_ls.acs_synonyms, &#39;&#39;),
                                base_name = nullif(st_ls.base_name, &#39;&#39;),
                                final = nullif(st_ls.final, &#39;&#39;),
                                naa_ccr_id = nullif(st_ls.naa_ccr_id, &#39;&#39;),
                                code_table = nullif(st_ls.code_table, &#39;&#39;),
                                is_set_root = nullif(st_ls.is_set_root, &#39;&#39;)::boolean,
                                panel_elements = nullif(st_ls.panel_elements, &#39;&#39;),
                                survey_question_text = nullif(st_ls.survey_question_text, &#39;&#39;),
                                survey_question_source = nullif(st_ls.survey_question_source, &#39;&#39;),
                                units_required = nullif(st_ls.units_required, &#39;&#39;),
                                submitted_units = nullif(st_ls.submitted_units, &#39;&#39;),
                                related_names_2 = nullif(st_ls.related_names_2, &#39;&#39;),
                                short_name = nullif(st_ls.short_name, &#39;&#39;),
                                order_obs = nullif(st_ls.order_obs, &#39;&#39;),
                                cdisc_common_tests = nullif(st_ls.cdisc_common_tests, &#39;&#39;),
                                hl7_field_subfield_id = nullif(st_ls.hl7_field_subfield_id, &#39;&#39;),
                                external_copyright_notice = nullif(st_ls.external_copyright_notice, &#39;&#39;),
                                example_units = nullif(st_ls.example_units, &#39;&#39;),
                                inpc_percentage = nullif(st_ls.inpc_percentage, &#39;&#39;),
                                long_common_name = nullif(st_ls.long_common_name, &#39;&#39;)
                        FROM
                                staging.loinc_staging st_ls
                        WHERE
                                fk_data_source = %(src_pk)s
                                        AND
                                code = nullif(st_ls.loinc_num, &#39;&#39;)
                                        AND
                                term = coalesce (
                                        nullif(st_ls.long_common_name, &#39;&#39;),
                                        (
                                                coalesce(nullif(st_ls.component, &#39;&#39;) || &#39;:&#39;, &#39;&#39;) ||
                                                coalesce(nullif(st_ls.property, &#39;&#39;) || &#39;:&#39;, &#39;&#39;) ||
                                                coalesce(nullif(st_ls.time_aspect, &#39;&#39;) || &#39;:&#39;, &#39;&#39;) ||
                                                coalesce(nullif(st_ls.system, &#39;&#39;) || &#39;:&#39;, &#39;&#39;) ||
                                                coalesce(nullif(st_ls.scale_type, &#39;&#39;) || &#39;:&#39;, &#39;&#39;) ||
                                                coalesce(nullif(st_ls.method_type, &#39;&#39;) || &#39;:&#39;, &#39;&#39;)
                                        )
                                )
                &#34;&#34;&#34;
        })
        curs = conn.cursor()
        gmPG2.run_rw_queries(link_obj = curs, queries = queries)
        curs.close()
        conn.commit()
        _log.debug(&#39;transfer from staging table to real table done&#39;)

        # clean out staging area
        curs = conn.cursor()
        cmd = &#34;&#34;&#34;DELETE FROM staging.loinc_staging&#34;&#34;&#34;
        gmPG2.run_rw_queries(link_obj = curs, queries = [{&#39;cmd&#39;: cmd}])
        curs.close()
        conn.commit()
        _log.debug(&#39;staging table emptied&#39;)

        return True

#============================================================
_SQL_LOINC_from_test_type = &#34;&#34;&#34;
        -- from test type
        SELECT
                loinc AS data,
                loinc AS field_label,
                (loinc || &#39;: &#39; || abbrev || &#39; (&#39; || name || &#39;)&#39;) AS list_label
        FROM clin.test_type
        WHERE loinc %(fragment_condition)s
&#34;&#34;&#34;

_SQL_LOINC_from_i18n_coded_term = &#34;&#34;&#34;
        -- from coded term, in user language
        SELECT
                code AS data,
                code AS field_label,
                (code || &#39;: &#39; || term) AS list_label
        FROM ref.v_coded_terms
        WHERE
                coding_system = &#39;LOINC&#39;
                        AND
                lang = i18n.get_curr_lang()
                        AND
                (code %(fragment_condition)s
                        OR
                term %(fragment_condition)s)
&#34;&#34;&#34;

_SQL_LOINC_from_en_EN_coded_term = &#34;&#34;&#34;
        -- from coded term, in English
        SELECT
                code AS data,
                code AS field_label,
                (code || &#39;: &#39; || term) AS list_label
        FROM ref.v_coded_terms
        WHERE
                coding_system = &#39;LOINC&#39;
                        AND
                lang = &#39;en_EN&#39;
                        AND
                (code %(fragment_condition)s
                        OR
                term %(fragment_condition)s)
&#34;&#34;&#34;

_SQL_LOINC_from_any_coded_term = &#34;&#34;&#34;
        -- from coded term, in any language
        SELECT
                code AS data,
                code AS field_label,
                (code || &#39;: &#39; || term) AS list_label
        FROM ref.v_coded_terms
        WHERE
                coding_system = &#39;LOINC&#39;
                        AND
                (code %(fragment_condition)s
                        OR
                term %(fragment_condition)s)
&#34;&#34;&#34;

#------------------------------------------------------------
class cLOINCMatchProvider(gmMatchProvider.cMatchProvider_SQL2):

        _pattern = regex.compile(r&#39;^\D+\s+\D+$&#39;, regex.UNICODE)

        _normal_query = &#34;&#34;&#34;
                SELECT DISTINCT ON (list_label)
                        data,
                        field_label,
                        list_label
                FROM (
                        (%s) UNION ALL (
                        %s)
                ) AS all_known_loinc&#34;&#34;&#34; % (
                        _SQL_LOINC_from_test_type,
                        _SQL_LOINC_from_any_coded_term
                )
#--                     %s) UNION ALL (
#--                     %s) UNION ALL (
#               %
#                       _SQL_LOINC_from_i18n_coded_term,
#                       _SQL_LOINC_from_en_EN_coded_term,

        #--------------------------------------------------------
        def getMatchesByPhrase(self, aFragment):
                &#34;&#34;&#34;Return matches for aFragment at start of phrases.&#34;&#34;&#34;

                self._queries = [cLOINCMatchProvider._normal_query + &#39;\nORDER BY list_label\nLIMIT 75&#39;]
                return gmMatchProvider.cMatchProvider_SQL2.getMatchesByPhrase(self, aFragment)

        #--------------------------------------------------------
        def getMatchesByWord(self, aFragment):
                &#34;&#34;&#34;Return matches for aFragment at start of words inside phrases.&#34;&#34;&#34;

                if cLOINCMatchProvider._pattern.match(aFragment):
                        fragmentA, fragmentB = aFragment.split(&#39; &#39;, 1)
                        query1 = cLOINCMatchProvider._normal_query % {&#39;fragment_condition&#39;: &#39;~* %%(fragmentA)s&#39;}
                        self._args[&#39;fragmentA&#39;] = &#34;( %s)|(^%s)&#34; % (fragmentA, fragmentA)
                        query2 = cLOINCMatchProvider._normal_query % {&#39;fragment_condition&#39;: &#39;~* %%(fragmentB)s&#39;}
                        self._args[&#39;fragmentB&#39;] = &#34;( %s)|(^%s)&#34; % (fragmentB, fragmentB)
                        self._queries = [&#34;SELECT * FROM (\n(%s\n) INTERSECT (%s)\n) AS intersected_matches\nORDER BY list_label\nLIMIT 75&#34; % (query1, query2)]
                        return self._find_matches(&#39;dummy&#39;)

                self._queries = [cLOINCMatchProvider._normal_query + &#39;\nORDER BY list_label\nLIMIT 75&#39;]
                return gmMatchProvider.cMatchProvider_SQL2.getMatchesByWord(self, aFragment)

        #--------------------------------------------------------
        def getMatchesBySubstr(self, aFragment):
                &#34;&#34;&#34;Return matches for aFragment as a true substring.&#34;&#34;&#34;

                if cLOINCMatchProvider._pattern.match(aFragment):
                        fragmentA, fragmentB = aFragment.split(&#39; &#39;, 1)
                        query1 = cLOINCMatchProvider._normal_query % {&#39;fragment_condition&#39;: &#34;ILIKE %%(fragmentA)s&#34;}
                        self._args[&#39;fragmentA&#39;] = &#39;%%%s%%&#39; % fragmentA
                        query2 = cLOINCMatchProvider._normal_query % {&#39;fragment_condition&#39;: &#34;ILIKE %%(fragmentB)s&#34;}
                        self._args[&#39;fragmentB&#39;] = &#39;%%%s%%&#39; % fragmentB
                        self._queries = [&#34;SELECT * FROM (\n(%s\n) INTERSECT (%s)\n) AS intersected_matches\nORDER BY list_label\nLIMIT 75&#34; % (query1, query2)]
                        return self._find_matches(&#39;dummy&#39;)

                self._queries = [cLOINCMatchProvider._normal_query + &#39;\nORDER BY list_label\nLIMIT 75&#39;]
                return gmMatchProvider.cMatchProvider_SQL2.getMatchesBySubstr(self, aFragment)

#============================================================
# main
#------------------------------------------------------------
if __name__ == &#34;__main__&#34;:

        if len(sys.argv) &lt; 2:
                sys.exit()

        if sys.argv[1] != &#39;test&#39;:
                sys.exit()

        from Gnumed.pycommon import gmI18N

        gmI18N.activate_locale()
#       gmDateTime.init()

        #--------------------------------------------------------
        def test_loinc_split():
                print(split_LOINCDBTXT(input_fname = sys.argv[2]))
        #--------------------------------------------------------
        def test_loinc_import():
                loinc_import(version = &#39;2.26&#39;)
        #--------------------------------------------------------
        def test_loinc2term():
                term = loinc2term(sys.argv[2])
                print(sys.argv[2], &#39;-&gt;&#39;, term)

        #--------------------------------------------------------
        def test_format_loinc():
                loinc = sys.argv[2]
                print(loinc)
                print(format_loinc(loinc))

        #--------------------------------------------------------
        #test_loinc_split()
        #test_loinc_import()
        #test_loinc2term()
        test_format_loinc()

#============================================================</code></pre>
</details>
</section>
<section>
</section>
<section>
</section>
<section>
<h2 class="section-title" id="header-functions">Functions</h2>
<dl>
<dt id="Gnumed.business.gmLOINC.format_loinc"><code class="name flex">
<span>def <span class="ident">format_loinc</span></span>(<span>loinc)</span>
</code></dt>
<dd>
<div class="desc"></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def format_loinc(loinc):
        data = loinc2data(loinc)
        if data is None:
                return None
        return gmTools.format_dict_like (
                dict(data),
                tabular = True,
                value_delimiters = None,
                values2ignore = [None, &#39;&#39;]
        )</code></pre>
</details>
</dd>
<dt id="Gnumed.business.gmLOINC.get_version"><code class="name flex">
<span>def <span class="ident">get_version</span></span>(<span>license_fname='loinc_license.txt')</span>
</code></dt>
<dd>
<div class="desc"></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def get_version(license_fname=&#39;loinc_license.txt&#39;):

        in_file = open(license_fname, mode = &#39;rt&#39;, encoding = &#39;utf-8-sig&#39;, errors = &#39;replace&#39;)

        version = None
        for line in in_file:
                if line.startswith(version_tag):
                        version = line[len(version_tag):].strip()
                        break

        in_file.close()
        return version</code></pre>
</details>
</dd>
<dt id="Gnumed.business.gmLOINC.loinc2data"><code class="name flex">
<span>def <span class="ident">loinc2data</span></span>(<span>loinc)</span>
</code></dt>
<dd>
<div class="desc"></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def loinc2data(loinc):
        cmd = &#39;SELECT * FROM ref.loinc WHERE code = %(loinc)s&#39;
        args = {&#39;loinc&#39;: loinc}
        rows = gmPG2.run_ro_queries(queries = [{&#39;cmd&#39;: cmd, &#39;args&#39;: args}])
        if len(rows) == 0:
                return None
        return rows[0]</code></pre>
</details>
</dd>
<dt id="Gnumed.business.gmLOINC.loinc2term"><code class="name flex">
<span>def <span class="ident">loinc2term</span></span>(<span>loinc=None)</span>
</code></dt>
<dd>
<div class="desc"></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def loinc2term(loinc=None):

        # NOTE: will return [NULL] on no-match due to the coalesce()
        cmd = &#34;&#34;&#34;
SELECT coalesce (
        (SELECT term
        FROM ref.v_coded_terms
        WHERE
                coding_system = &#39;LOINC&#39;
                        AND
                code = %(loinc)s
                        AND
                lang = i18n.get_curr_lang()
        ),
        (SELECT term
        FROM ref.v_coded_terms
        WHERE
                coding_system = &#39;LOINC&#39;
                        AND
                code = %(loinc)s
                        AND
                lang = &#39;en_EN&#39;
        ),
        (SELECT term
        FROM ref.v_coded_terms
        WHERE
                coding_system = &#39;LOINC&#39;
                        AND
                code = %(loinc)s
        )
)&#34;&#34;&#34;
        args = {&#39;loinc&#39;: loinc}
        rows = gmPG2.run_ro_queries(queries = [{&#39;cmd&#39;: cmd, &#39;args&#39;: args}])

        if rows[0][0] is None:
                return []

        return [ r[0] for r in rows ]</code></pre>
</details>
</dd>
<dt id="Gnumed.business.gmLOINC.loinc_import"><code class="name flex">
<span>def <span class="ident">loinc_import</span></span>(<span>data_fname=None, license_fname=None, version=None, conn=None, lang='en_EN')</span>
</code></dt>
<dd>
<div class="desc"></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def loinc_import(data_fname=None, license_fname=None, version=None, conn=None, lang=&#39;en_EN&#39;):

        if version is None:
                version = get_version(license_fname = license_fname)

        if version is None:
                raise ValueError(&#39;cannot detect LOINC version&#39;)

        _log.debug(&#39;importing LOINC version [%s]&#39;, version)

        # clean out staging area
        curs = conn.cursor()
        cmd = &#34;&#34;&#34;DELETE FROM staging.loinc_staging&#34;&#34;&#34;
        gmPG2.run_rw_queries(link_obj = curs, queries = [{&#39;cmd&#39;: cmd}])
        curs.close()
        conn.commit()
        _log.debug(&#39;staging table emptied&#39;)

        # import data from csv file into staging table
        csv_file = open(data_fname, mode = &#39;rt&#39;, encoding = &#39;utf-8-sig&#39;, errors = &#39;replace&#39;)
        loinc_reader = gmTools.unicode_csv_reader(csv_file, delimiter = &#34;\t&#34;, quotechar = &#39;&#34;&#39;)
        curs = conn.cursor()
        cmd = &#34;&#34;&#34;INSERT INTO staging.loinc_staging values (%s%%s)&#34;&#34;&#34; % (&#39;%s, &#39; * (len(loinc_fields) - 1))
        first = False
        for loinc_line in loinc_reader:
                if not first:
                        first = True
                        continue
                gmPG2.run_rw_queries(link_obj = curs, queries = [{&#39;cmd&#39;: cmd, &#39;args&#39;: loinc_line}])
        curs.close()
        conn.commit()
        csv_file.close()
        _log.debug(&#39;staging table loaded&#39;)

        # create data source record
        in_file = open(license_fname, mode = &#39;rt&#39;, encoding = &#39;utf-8-sig&#39;, errors = &#39;replace&#39;)
        desc = in_file.read()
        in_file.close()
        args = {&#39;ver&#39;: version, &#39;desc&#39;: desc, &#39;url&#39;: origin_url, &#39;name_long&#39;: name_long, &#39;name_short&#39;: name_short, &#39;lang&#39;: lang}
        queries = [
                # insert if not existing
                {&#39;args&#39;: args, &#39;cmd&#39;: &#34;&#34;&#34;
                        INSERT INTO ref.data_source (name_long, name_short, version) SELECT
                                %(name_long)s,
                                %(name_short)s,
                                %(ver)s
                        WHERE NOT EXISTS (
                                SELECT 1 FROM ref.data_source WHERE
                                        name_long = %(name_long)s
                                                AND
                                        name_short = %(name_short)s
                                                AND
                                        version = %(ver)s
                        )&#34;&#34;&#34;
                },
                # update non-unique fields
                {&#39;args&#39;: args, &#39;cmd&#39;: &#34;&#34;&#34;
                        UPDATE ref.data_source SET
                                description = %(desc)s,
                                source = %(url)s,
                                lang = %(lang)s
                        WHERE
                                name_long = %(name_long)s
                                        AND
                                name_short = %(name_short)s
                                        AND
                                version = %(ver)s
                        &#34;&#34;&#34;
                },
                # retrieve PK of data source
                {&#39;args&#39;: args, &#39;cmd&#39;: &#34;&#34;&#34;SELECT pk FROM ref.data_source WHERE name_short = %(name_short)s AND version = %(ver)s&#34;&#34;&#34;}
        ]
        curs = conn.cursor()
        rows = gmPG2.run_rw_queries(link_obj = curs, queries = queries, return_data = True)
        data_src_pk = rows[0][0]
        curs.close()
        _log.debug(&#39;data source record created or updated, pk is #%s&#39;, data_src_pk)

        # import from staging table to real table
        args = {&#39;src_pk&#39;: data_src_pk}
        queries = []
        queries.append ({
                &#39;args&#39;: args,
                &#39;cmd&#39;: &#34;&#34;&#34;
                        INSERT INTO ref.loinc (
                                fk_data_source, term, code
                        )
                        SELECT
                                %(src_pk)s,
                                coalesce (
                                        nullif(long_common_name, &#39;&#39;),
                                        (
                                                coalesce(nullif(component, &#39;&#39;) || &#39;:&#39;, &#39;&#39;) ||
                                                coalesce(nullif(property, &#39;&#39;) || &#39;:&#39;, &#39;&#39;) ||
                                                coalesce(nullif(time_aspect, &#39;&#39;) || &#39;:&#39;, &#39;&#39;) ||
                                                coalesce(nullif(system, &#39;&#39;) || &#39;:&#39;, &#39;&#39;) ||
                                                coalesce(nullif(scale_type, &#39;&#39;) || &#39;:&#39;, &#39;&#39;) ||
                                                coalesce(nullif(method_type, &#39;&#39;) || &#39;:&#39;, &#39;&#39;)
                                        )
                                ),
                                nullif(loinc_num, &#39;&#39;)
                        FROM
                                staging.loinc_staging st_ls
                        WHERE NOT EXISTS (
                                SELECT 1 FROM ref.loinc r_l WHERE
                                        r_l.fk_data_source = %(src_pk)s
                                                AND
                                        r_l.code = nullif(st_ls.loinc_num, &#39;&#39;)
                                                AND
                                        r_l.term =      coalesce (
                                                nullif(st_ls.long_common_name, &#39;&#39;),
                                                (
                                                        coalesce(nullif(st_ls.component, &#39;&#39;) || &#39;:&#39;, &#39;&#39;) ||
                                                        coalesce(nullif(st_ls.property, &#39;&#39;) || &#39;:&#39;, &#39;&#39;) ||
                                                        coalesce(nullif(st_ls.time_aspect, &#39;&#39;) || &#39;:&#39;, &#39;&#39;) ||
                                                        coalesce(nullif(st_ls.system, &#39;&#39;) || &#39;:&#39;, &#39;&#39;) ||
                                                        coalesce(nullif(st_ls.scale_type, &#39;&#39;) || &#39;:&#39;, &#39;&#39;) ||
                                                        coalesce(nullif(st_ls.method_type, &#39;&#39;) || &#39;:&#39;, &#39;&#39;)
                                                )
                                        )
                        )&#34;&#34;&#34;
        })
        queries.append ({
                &#39;args&#39;: args,
                &#39;cmd&#39;: &#34;&#34;&#34;
                        UPDATE ref.loinc SET
                                comment = nullif(st_ls.comments, &#39;&#39;),
                                component = nullif(st_ls.component, &#39;&#39;),
                                property = nullif(st_ls.property, &#39;&#39;),
                                time_aspect = nullif(st_ls.time_aspect, &#39;&#39;),
                                system = nullif(st_ls.system, &#39;&#39;),
                                scale_type = nullif(st_ls.scale_type, &#39;&#39;),
                                method_type = nullif(st_ls.method_type, &#39;&#39;),
                                related_names_1_old = nullif(st_ls.related_names_1_old, &#39;&#39;),
                                grouping_class = nullif(st_ls.class, &#39;&#39;),
                                loinc_internal_source = nullif(st_ls.source, &#39;&#39;),
                                dt_last_change = nullif(st_ls.dt_last_change, &#39;&#39;),
                                change_type = nullif(st_ls.change_type, &#39;&#39;),
                                answer_list = nullif(st_ls.answer_list, &#39;&#39;),
                                code_status = nullif(st_ls.status, &#39;&#39;),
                                maps_to = nullif(st_ls.map_to, &#39;&#39;),
                                scope = nullif(st_ls.scope, &#39;&#39;),
                                normal_range = nullif(st_ls.normal_range, &#39;&#39;),
                                ipcc_units = nullif(st_ls.ipcc_units, &#39;&#39;),
                                reference = nullif(st_ls.reference, &#39;&#39;),
                                exact_component_synonym = nullif(st_ls.exact_component_synonym, &#39;&#39;),
                                molar_mass = nullif(st_ls.molar_mass, &#39;&#39;),
                                grouping_class_type = nullif(st_ls.class_type, &#39;&#39;)::smallint,
                                formula = nullif(st_ls.formula, &#39;&#39;),
                                species = nullif(st_ls.species, &#39;&#39;),
                                example_answers = nullif(st_ls.example_answers, &#39;&#39;),
                                acs_synonyms = nullif(st_ls.acs_synonyms, &#39;&#39;),
                                base_name = nullif(st_ls.base_name, &#39;&#39;),
                                final = nullif(st_ls.final, &#39;&#39;),
                                naa_ccr_id = nullif(st_ls.naa_ccr_id, &#39;&#39;),
                                code_table = nullif(st_ls.code_table, &#39;&#39;),
                                is_set_root = nullif(st_ls.is_set_root, &#39;&#39;)::boolean,
                                panel_elements = nullif(st_ls.panel_elements, &#39;&#39;),
                                survey_question_text = nullif(st_ls.survey_question_text, &#39;&#39;),
                                survey_question_source = nullif(st_ls.survey_question_source, &#39;&#39;),
                                units_required = nullif(st_ls.units_required, &#39;&#39;),
                                submitted_units = nullif(st_ls.submitted_units, &#39;&#39;),
                                related_names_2 = nullif(st_ls.related_names_2, &#39;&#39;),
                                short_name = nullif(st_ls.short_name, &#39;&#39;),
                                order_obs = nullif(st_ls.order_obs, &#39;&#39;),
                                cdisc_common_tests = nullif(st_ls.cdisc_common_tests, &#39;&#39;),
                                hl7_field_subfield_id = nullif(st_ls.hl7_field_subfield_id, &#39;&#39;),
                                external_copyright_notice = nullif(st_ls.external_copyright_notice, &#39;&#39;),
                                example_units = nullif(st_ls.example_units, &#39;&#39;),
                                inpc_percentage = nullif(st_ls.inpc_percentage, &#39;&#39;),
                                long_common_name = nullif(st_ls.long_common_name, &#39;&#39;)
                        FROM
                                staging.loinc_staging st_ls
                        WHERE
                                fk_data_source = %(src_pk)s
                                        AND
                                code = nullif(st_ls.loinc_num, &#39;&#39;)
                                        AND
                                term = coalesce (
                                        nullif(st_ls.long_common_name, &#39;&#39;),
                                        (
                                                coalesce(nullif(st_ls.component, &#39;&#39;) || &#39;:&#39;, &#39;&#39;) ||
                                                coalesce(nullif(st_ls.property, &#39;&#39;) || &#39;:&#39;, &#39;&#39;) ||
                                                coalesce(nullif(st_ls.time_aspect, &#39;&#39;) || &#39;:&#39;, &#39;&#39;) ||
                                                coalesce(nullif(st_ls.system, &#39;&#39;) || &#39;:&#39;, &#39;&#39;) ||
                                                coalesce(nullif(st_ls.scale_type, &#39;&#39;) || &#39;:&#39;, &#39;&#39;) ||
                                                coalesce(nullif(st_ls.method_type, &#39;&#39;) || &#39;:&#39;, &#39;&#39;)
                                        )
                                )
                &#34;&#34;&#34;
        })
        curs = conn.cursor()
        gmPG2.run_rw_queries(link_obj = curs, queries = queries)
        curs.close()
        conn.commit()
        _log.debug(&#39;transfer from staging table to real table done&#39;)

        # clean out staging area
        curs = conn.cursor()
        cmd = &#34;&#34;&#34;DELETE FROM staging.loinc_staging&#34;&#34;&#34;
        gmPG2.run_rw_queries(link_obj = curs, queries = [{&#39;cmd&#39;: cmd}])
        curs.close()
        conn.commit()
        _log.debug(&#39;staging table emptied&#39;)

        return True</code></pre>
</details>
</dd>
<dt id="Gnumed.business.gmLOINC.map_field_names"><code class="name flex">
<span>def <span class="ident">map_field_names</span></span>(<span>data_fname='loinc_data.csv')</span>
</code></dt>
<dd>
<div class="desc"></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def map_field_names(data_fname=&#39;loinc_data.csv&#39;):

        csv_file = open(data_fname, mode = &#39;rt&#39;, encoding = &#39;utf-8-sig&#39;, errors = &#39;replace&#39;)
        first_line = csv_file.readline()
        sniffer = csv.Sniffer()
        if sniffer.has_header(first_line):
                pass</code></pre>
</details>
</dd>
<dt id="Gnumed.business.gmLOINC.split_LOINCDBTXT"><code class="name flex">
<span>def <span class="ident">split_LOINCDBTXT</span></span>(<span>input_fname=None, data_fname=None, license_fname=None)</span>
</code></dt>
<dd>
<div class="desc"></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def split_LOINCDBTXT(input_fname=None, data_fname=None, license_fname=None):

        _log.debug(&#39;splitting LOINC source file [%s]&#39;, input_fname)

        if license_fname is None:
                license_fname = gmTools.get_unique_filename(prefix = &#39;loinc_license-&#39;, suffix = &#39;.txt&#39;)
        _log.debug(&#39;LOINC header: %s&#39;, license_fname)

        if data_fname is None:
                data_fname = gmTools.get_unique_filename(prefix = &#39;loinc_data-&#39;, suffix = &#39;.csv&#39;)
        _log.debug(&#39;LOINC data: %s&#39;, data_fname)

        loinc_file = open(input_fname, mode = &#39;rt&#39;, encoding = file_encoding, errors = &#39;replace&#39;)
        out_file = open(license_fname, mode = &#39;wt&#39;, encoding = &#39;utf8&#39;, errors = &#39;replace&#39;)

        for line in loinc_file:

                if license_delimiter in line:
                        out_file.write(line)
                        out_file.close()
                        out_file = open(data_fname, mode = &#39;wt&#39;, encoding = &#39;utf8&#39;, errors = &#39;replace&#39;)
                        continue

                out_file.write(line)

        out_file.close()

        return data_fname, license_fname</code></pre>
</details>
</dd>
</dl>
</section>
<section>
<h2 class="section-title" id="header-classes">Classes</h2>
<dl>
<dt id="Gnumed.business.gmLOINC.cLOINCMatchProvider"><code class="flex name class">
<span>class <span class="ident">cLOINCMatchProvider</span></span>
<span>(</span><span>queries=None, context=None)</span>
</code></dt>
<dd>
<div class="desc"><p>Match provider which searches matches
in possibly several database tables.</p>
<p>queries:
- a list of unicode strings
- each string is a query
- each string must contain: "&hellip; WHERE <column> %(fragment_condition)s &hellip;"
- each string can contain in the where clause: "&hellip; %(<ctxt_key1>)s &hellip;"
- each query must return (data, list_label, field_label)</p>
<p>context definitions to be used in the queries, example:
{'ctxt_key1': {'where_part': 'AND country = %(country)s', 'placeholder': 'country'}}</p>
<p>client code using .set_context() must use the 'placeholder':
<phrasewheel>/<match provider>.set_context('country', 'Germany')</p>
<p>full example query:</p>
<pre><code>    query = u" " "
            SELECT DISTINCT ON (list_label)
                    pk_encounter
                            AS data,
                    to_char(started, 'YYYY Mon DD (HH24:MI)') || ': ' || l10n_type || ' [#' || pk_encounter || ']'
                            AS list_label,
                    to_char(started, 'YYYY Mon DD') || ': ' || l10n_type
                            AS field_label
            FROM
                    clin.v_pat_encounters
            WHERE
                    (
                            l10n_type %(fragment_condition)s
                                    OR
                            type %(fragment_condition)s
                    )       %(ctxt_patient)s
            ORDER BY
                    list_label
            LIMIT
                    30
    " " "
    context = {'ctxt_patient': {
            'where_part': u'AND pk_patient = %(PLACEHOLDER)s',
            'placeholder': u'PLACEHOLDER'
    }}
    self.mp = gmMatchProvider.cMatchProvider_SQL2(queries = query, context = context)
    self.set_context(context = 'PLACEHOLDER', val = '&lt;THE VALUE&gt;')
</code></pre>
<p>_SQL_data2match:
SQL to retrieve a match by, say, primary key
wherein the only keyword argument is 'pk'</p></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">class cLOINCMatchProvider(gmMatchProvider.cMatchProvider_SQL2):

        _pattern = regex.compile(r&#39;^\D+\s+\D+$&#39;, regex.UNICODE)

        _normal_query = &#34;&#34;&#34;
                SELECT DISTINCT ON (list_label)
                        data,
                        field_label,
                        list_label
                FROM (
                        (%s) UNION ALL (
                        %s)
                ) AS all_known_loinc&#34;&#34;&#34; % (
                        _SQL_LOINC_from_test_type,
                        _SQL_LOINC_from_any_coded_term
                )
#--                     %s) UNION ALL (
#--                     %s) UNION ALL (
#               %
#                       _SQL_LOINC_from_i18n_coded_term,
#                       _SQL_LOINC_from_en_EN_coded_term,

        #--------------------------------------------------------
        def getMatchesByPhrase(self, aFragment):
                &#34;&#34;&#34;Return matches for aFragment at start of phrases.&#34;&#34;&#34;

                self._queries = [cLOINCMatchProvider._normal_query + &#39;\nORDER BY list_label\nLIMIT 75&#39;]
                return gmMatchProvider.cMatchProvider_SQL2.getMatchesByPhrase(self, aFragment)

        #--------------------------------------------------------
        def getMatchesByWord(self, aFragment):
                &#34;&#34;&#34;Return matches for aFragment at start of words inside phrases.&#34;&#34;&#34;

                if cLOINCMatchProvider._pattern.match(aFragment):
                        fragmentA, fragmentB = aFragment.split(&#39; &#39;, 1)
                        query1 = cLOINCMatchProvider._normal_query % {&#39;fragment_condition&#39;: &#39;~* %%(fragmentA)s&#39;}
                        self._args[&#39;fragmentA&#39;] = &#34;( %s)|(^%s)&#34; % (fragmentA, fragmentA)
                        query2 = cLOINCMatchProvider._normal_query % {&#39;fragment_condition&#39;: &#39;~* %%(fragmentB)s&#39;}
                        self._args[&#39;fragmentB&#39;] = &#34;( %s)|(^%s)&#34; % (fragmentB, fragmentB)
                        self._queries = [&#34;SELECT * FROM (\n(%s\n) INTERSECT (%s)\n) AS intersected_matches\nORDER BY list_label\nLIMIT 75&#34; % (query1, query2)]
                        return self._find_matches(&#39;dummy&#39;)

                self._queries = [cLOINCMatchProvider._normal_query + &#39;\nORDER BY list_label\nLIMIT 75&#39;]
                return gmMatchProvider.cMatchProvider_SQL2.getMatchesByWord(self, aFragment)

        #--------------------------------------------------------
        def getMatchesBySubstr(self, aFragment):
                &#34;&#34;&#34;Return matches for aFragment as a true substring.&#34;&#34;&#34;

                if cLOINCMatchProvider._pattern.match(aFragment):
                        fragmentA, fragmentB = aFragment.split(&#39; &#39;, 1)
                        query1 = cLOINCMatchProvider._normal_query % {&#39;fragment_condition&#39;: &#34;ILIKE %%(fragmentA)s&#34;}
                        self._args[&#39;fragmentA&#39;] = &#39;%%%s%%&#39; % fragmentA
                        query2 = cLOINCMatchProvider._normal_query % {&#39;fragment_condition&#39;: &#34;ILIKE %%(fragmentB)s&#34;}
                        self._args[&#39;fragmentB&#39;] = &#39;%%%s%%&#39; % fragmentB
                        self._queries = [&#34;SELECT * FROM (\n(%s\n) INTERSECT (%s)\n) AS intersected_matches\nORDER BY list_label\nLIMIT 75&#34; % (query1, query2)]
                        return self._find_matches(&#39;dummy&#39;)

                self._queries = [cLOINCMatchProvider._normal_query + &#39;\nORDER BY list_label\nLIMIT 75&#39;]
                return gmMatchProvider.cMatchProvider_SQL2.getMatchesBySubstr(self, aFragment)</code></pre>
</details>
<h3>Ancestors</h3>
<ul class="hlist">
<li><a title="Gnumed.pycommon.gmMatchProvider.cMatchProvider_SQL2" href="gmMatchProvider.html#Gnumed.pycommon.gmMatchProvider.cMatchProvider_SQL2">cMatchProvider_SQL2</a></li>
<li><a title="Gnumed.pycommon.gmMatchProvider.cMatchProvider" href="gmMatchProvider.html#Gnumed.pycommon.gmMatchProvider.cMatchProvider">cMatchProvider</a></li>
</ul>
<h3>Inherited members</h3>
<ul class="hlist">
<li><code><b><a title="Gnumed.pycommon.gmMatchProvider.cMatchProvider_SQL2" href="gmMatchProvider.html#Gnumed.pycommon.gmMatchProvider.cMatchProvider_SQL2">cMatchProvider_SQL2</a></b></code>:
<ul class="hlist">
<li><code><a title="Gnumed.pycommon.gmMatchProvider.cMatchProvider_SQL2.getAllMatches" href="gmMatchProvider.html#Gnumed.pycommon.gmMatchProvider.cMatchProvider_SQL2.getAllMatches">getAllMatches</a></code></li>
<li><code><a title="Gnumed.pycommon.gmMatchProvider.cMatchProvider_SQL2.getMatches" href="gmMatchProvider.html#Gnumed.pycommon.gmMatchProvider.cMatchProvider.getMatches">getMatches</a></code></li>
<li><code><a title="Gnumed.pycommon.gmMatchProvider.cMatchProvider_SQL2.getMatchesByPhrase" href="gmMatchProvider.html#Gnumed.pycommon.gmMatchProvider.cMatchProvider_SQL2.getMatchesByPhrase">getMatchesByPhrase</a></code></li>
<li><code><a title="Gnumed.pycommon.gmMatchProvider.cMatchProvider_SQL2.getMatchesBySubstr" href="gmMatchProvider.html#Gnumed.pycommon.gmMatchProvider.cMatchProvider_SQL2.getMatchesBySubstr">getMatchesBySubstr</a></code></li>
<li><code><a title="Gnumed.pycommon.gmMatchProvider.cMatchProvider_SQL2.getMatchesByWord" href="gmMatchProvider.html#Gnumed.pycommon.gmMatchProvider.cMatchProvider_SQL2.getMatchesByWord">getMatchesByWord</a></code></li>
<li><code><a title="Gnumed.pycommon.gmMatchProvider.cMatchProvider_SQL2.setThresholds" href="gmMatchProvider.html#Gnumed.pycommon.gmMatchProvider.cMatchProvider.setThresholds">setThresholds</a></code></li>
<li><code><a title="Gnumed.pycommon.gmMatchProvider.cMatchProvider_SQL2.set_context" href="gmMatchProvider.html#Gnumed.pycommon.gmMatchProvider.cMatchProvider.set_context">set_context</a></code></li>
</ul>
</li>
</ul>
</dd>
</dl>
</section>
</article>
<nav id="sidebar">
<h1>Index</h1>
<div class="toc">
<ul></ul>
</div>
<ul id="index">
<li><h3>Super-module</h3>
<ul>
<li><code><a title="Gnumed.business" href="http://www.gnumed.de/downloads/docs/api/business/index.html">Gnumed.business</a></code></li>
</ul>
</li>
<li><h3><a href="gmLOINC.html#header-functions">Functions</a></h3>
<ul class="two-column">
<li><code><a title="Gnumed.business.gmLOINC.format_loinc" href="gmLOINC.html#Gnumed.business.gmLOINC.format_loinc">format_loinc</a></code></li>
<li><code><a title="Gnumed.business.gmLOINC.get_version" href="gmLOINC.html#Gnumed.business.gmLOINC.get_version">get_version</a></code></li>
<li><code><a title="Gnumed.business.gmLOINC.loinc2data" href="gmLOINC.html#Gnumed.business.gmLOINC.loinc2data">loinc2data</a></code></li>
<li><code><a title="Gnumed.business.gmLOINC.loinc2term" href="gmLOINC.html#Gnumed.business.gmLOINC.loinc2term">loinc2term</a></code></li>
<li><code><a title="Gnumed.business.gmLOINC.loinc_import" href="gmLOINC.html#Gnumed.business.gmLOINC.loinc_import">loinc_import</a></code></li>
<li><code><a title="Gnumed.business.gmLOINC.map_field_names" href="gmLOINC.html#Gnumed.business.gmLOINC.map_field_names">map_field_names</a></code></li>
<li><code><a title="Gnumed.business.gmLOINC.split_LOINCDBTXT" href="gmLOINC.html#Gnumed.business.gmLOINC.split_LOINCDBTXT">split_LOINCDBTXT</a></code></li>
</ul>
</li>
<li><h3><a href="gmLOINC.html#header-classes">Classes</a></h3>
<ul>
<li>
<h4><code><a title="Gnumed.business.gmLOINC.cLOINCMatchProvider" href="gmLOINC.html#Gnumed.business.gmLOINC.cLOINCMatchProvider">cLOINCMatchProvider</a></code></h4>
</li>
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