RunasSudo
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MedicineSearch
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Separate MP, MPP information into separate table

This commit is contained in:
RunasSudo 2023-01-24 18:57:30 +11:00
parent e57518e37b
commit 8967b3e5b9
Signed by: RunasSudo
GPG Key ID: 7234E476BF21C61A
3 changed files with 47 additions and 11 deletions
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2
export_db.sh
View File

@ -1,4 +1,4 @@
#!/bin/bash
rm html/database.db
sqlite3 database.db '.dump pbs_item pbs_item_restriction pbs_restriction pbs_restriction_criteria pbs_criteria pbs_criteria_parameter' | sqlite3 html/database.db
sqlite3 database.db '.dump pbs_item pbs_mp pbs_mpp pbs_item_restriction pbs_restriction pbs_restriction_criteria pbs_criteria pbs_criteria_parameter' | sqlite3 html/database.db

4
html/index.html
View File

@ -76,7 +76,7 @@
db = new SQL.Database(new Uint8Array(buf));
// Initialise search bar
const labels = execAsScalars(db.prepare('SELECT DISTINCT mp_preferred_term FROM pbs_item ORDER BY LOWER(mp_preferred_term)'));
const labels = execAsScalars(db.prepare('SELECT DISTINCT preferred_term FROM pbs_mp ORDER BY LOWER(preferred_term)'));
const data = labels.map(label => ({'label': label}));
const autocomplete = new Autocomplete(document.getElementById('search-input'), {
data: data,
@ -88,7 +88,7 @@
function onClickSearchItem(item) {
// Find matching PBS items
let stmt = db.prepare('SELECT * FROM pbs_item WHERE LOWER(mp_preferred_term) = ?');
let stmt = db.prepare('SELECT * FROM pbs_item LEFT JOIN (SELECT code AS mpp_code, preferred_term AS mpp_preferred_term, mp_code FROM pbs_mpp) AS pbs_mpp ON pbs_item.mpp_code = pbs_mpp.mpp_code LEFT JOIN (SELECT code AS mp_code, preferred_term AS mp_preferred_term FROM pbs_mp) AS pbs_mp ON pbs_mpp.mp_code = pbs_mp.mp_code WHERE LOWER(mp_preferred_term) = ?');
stmt.bind([item.label.toLowerCase()]);
const items = execAsObjects(stmt);

52
import_pbs_xml.py
View File

@ -23,7 +23,13 @@ cur = con.cursor()
# Init schema
cur.execute('DROP TABLE IF EXISTS pbs_item')
cur.execute('CREATE TABLE pbs_item (code TEXT PRIMARY KEY, mpp_preferred_term TEXT, mp_preferred_term TEXT, maximum_prescribable_units INTEGER, number_repeats INTEGER, benefit_type TEXT)')
cur.execute('CREATE TABLE pbs_item (code TEXT PRIMARY KEY, mpp_code TEXT, maximum_prescribable_units INTEGER, number_repeats INTEGER, benefit_type TEXT)')
cur.execute('DROP TABLE IF EXISTS pbs_mpp')
cur.execute('CREATE TABLE pbs_mpp (code TEXT PRIMARY KEY, mp_code TEXT, preferred_term TEXT)')
cur.execute('DROP TABLE IF EXISTS pbs_mp')
cur.execute('CREATE TABLE pbs_mp (code TEXT PRIMARY KEY, preferred_term TEXT)')
cur.execute('DROP TABLE IF EXISTS pbs_item_restriction')
cur.execute('CREATE TABLE pbs_item_restriction (item_code TEXT, restriction_code INTEGER)')
@ -53,6 +59,8 @@ ns = {'pbs': 'http://schema.pbs.gov.au/', 'xlink': 'http://www.w3.org/1999/xlink
# Get General Schedule
program = next(p for p in root.find('pbs:schedule', ns).findall('pbs:program', ns) if p.find('pbs:info', ns).find('pbs:code', ns).text == 'GE')
mpps_to_parse = set()
mps_to_parse = set()
restrictions_to_parse = set()
criteria_to_parse = set()
@ -70,12 +78,7 @@ for item in program.findall('pbs:prescribing-rule', ns):
benefit = benefits[0]
mpp_id = item.find('pbs:ready-prepared', ns).find('pbs:mpp-reference', ns).get('{http://www.w3.org/1999/xlink}href').lstrip('#')
mpp = root.find('pbs:drugs-list', ns).find('pbs:mpp[@xml:id="' + mpp_id + '"]', ns)
mpp_preferred_term = mpp.find('pbs:preferred-term', ns).text
mp_id = mpp.find('pbs:drug-references-list', ns).find('pbs:mp-reference', ns).get('{http://www.w3.org/1999/xlink}href').lstrip('#')
mp = root.find('pbs:drugs-list', ns).find('pbs:mp[@xml:id="' + mp_id + '"]', ns)
mp_preferred_term = mp.find('pbs:preferred-term[@rdf:resource="http://pbs.gov.au/clinical"]', ns).text
mpp_code = item.find('pbs:ready-prepared', ns).find('pbs:mpp-reference', ns).find('pbs:code', ns).text
max_units = item.find('pbs:ready-prepared', ns).find('pbs:maximum-prescribable[@rdf:resource="http://pbs.gov.au/reference/unit-of-use"]', ns).find('pbs:value', ns).text
max_repeats = item.find('pbs:ready-prepared', ns).find('pbs:number-repeats', ns).find('pbs:value', ns).text
@ -87,7 +90,7 @@ for item in program.findall('pbs:prescribing-rule', ns):
'http://pbs.gov.au/benefit-type/authority-required': 'authority',
}[benefit.get('{http://www.w3.org/1999/02/22-rdf-syntax-ns#}resource')]
cur.execute('INSERT INTO pbs_item (code, mpp_preferred_term, mp_preferred_term, maximum_prescribable_units, number_repeats, benefit_type) VALUES (?, ?, ?, ?, ?, ?)', (code, mpp_preferred_term, mp_preferred_term, max_units, max_repeats, benefit_type))
cur.execute('INSERT INTO pbs_item (code, mpp_code, maximum_prescribable_units, number_repeats, benefit_type) VALUES (?, ?, ?, ?, ?)', (code, mpp_code, max_units, max_repeats, benefit_type))
# Get restrictions
if restrictions := benefit.find('pbs:restriction-references-list', ns):
@ -98,6 +101,39 @@ for item in program.findall('pbs:prescribing-rule', ns):
# Queue this restriction for parsing
restrictions_to_parse.add(restriction_id)
# Queue the MPP for parsing
mpps_to_parse.add(mpp_id)
# Parse MPPs
for mpp_id in sorted(list(mpps_to_parse)):
mpp = root.find('pbs:drugs-list', ns).find('pbs:mpp[@xml:id="' + mpp_id + '"]', ns)
mpp_code = mpp.find('pbs:code', ns).text
mpp_preferred_term = mpp.find('pbs:preferred-term', ns).text
mp_id = mpp.find('pbs:drug-references-list', ns).find('pbs:mp-reference', ns).get('{http://www.w3.org/1999/xlink}href').lstrip('#')
mp = root.find('pbs:drugs-list', ns).find('pbs:mp[@xml:id="' + mp_id + '"]', ns)
mp_code = mp.find('pbs:code[@rdf:resource="http://pbs.gov.au/Drug/MP"]', ns).text # Must look this up because the <code> in <mp-reference> is only SNOMED
cur.execute('INSERT INTO pbs_mpp (code, mp_code, preferred_term) VALUES (?, ?, ?)', (mpp_code, mp_code, mpp_preferred_term))
# Queue the MP for parsing
mps_to_parse.add(mp_id)
# Get TPPs
for tpp_reference in mpp.find('pbs:drug-references-list', ns).findall('pbs:tpp-reference', ns):
tpp_id = tpp_reference.get('{http://www.w3.org/1999/xlink}href').lstrip('#')
# Queue the TPP for parsing
tpps_to_parse.add((tpp_id, mpp_code))
# Parse MPs
for mp_id in sorted(list(mps_to_parse)):
mp = root.find('pbs:drugs-list', ns).find('pbs:mp[@xml:id="' + mp_id + '"]', ns)
mp_code = mp.find('pbs:code[@rdf:resource="http://pbs.gov.au/Drug/MP"]', ns).text # Also there are SNOMED codes but they are inconsistent
mp_preferred_term = mp.find('pbs:preferred-term[@rdf:resource="http://pbs.gov.au/clinical"]', ns).text
cur.execute('INSERT INTO pbs_mp (code, preferred_term) VALUES (?, ?)', (mp_code, mp_preferred_term))
# Parse restrictions
for restriction_id in sorted(list(restrictions_to_parse)):