Read PBS data from XML file
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@ -1,4 +1,4 @@
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#!/bin/bash
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rm html/database.db
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sqlite3 database.db '.dump pbs_drug pbs_prescriber_type pbs_streamlined' | sqlite3 html/database.db
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sqlite3 database.db '.dump pbs_item pbs_item_restriction pbs_restriction pbs_restriction_criteria pbs_criteria pbs_criteria_parameter' | sqlite3 html/database.db
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@ -72,7 +72,7 @@
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db = new SQL.Database(new Uint8Array(buf));
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// Initialise search bar
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const labels = execAsScalars(db.prepare('SELECT DISTINCT mp_pt FROM pbs_drug ORDER BY LOWER(mp_pt)'));
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const labels = execAsScalars(db.prepare('SELECT DISTINCT mp_preferred_term FROM pbs_item ORDER BY LOWER(mp_preferred_term)'));
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const data = labels.map(label => ({'label': label}));
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const autocomplete = new Autocomplete(document.getElementById('search-input'), {
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data: data,
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@ -84,7 +84,7 @@
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function onClickSearchItem(item) {
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// Find matching PBS items
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const stmt = db.prepare('SELECT *, (SELECT COUNT(1) FROM pbs_streamlined WHERE pbs_drug.item_code = pbs_streamlined.item_code) AS streamlined_authorities FROM pbs_drug LEFT JOIN pbs_prescriber_type ON pbs_drug.item_code = pbs_prescriber_type.item_code WHERE LOWER(mp_pt) = ? AND prescriber_type = "M"');
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const stmt = db.prepare('SELECT * FROM pbs_item WHERE LOWER(mp_preferred_term) = ?');
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stmt.bind([item.label.toLowerCase()]);
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const items = execAsObjects(stmt);
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@ -95,26 +95,25 @@
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tbody.innerHTML = '';
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for (let item of items) {
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const tr = document.createElement('tr');
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let td = document.createElement('td'); td.innerHTML = '<a href="https://www.pbs.gov.au/medicine/item/' + item['item_code'] + '" target="_blank">' + item['item_code'] + '</a>'; tr.appendChild(td);
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td = document.createElement('td'); td.innerText = item['tpuu_or_mpp_pt']; tr.appendChild(td);
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td = document.createElement('td'); td.innerText = item['mq']; tr.appendChild(td);
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td = document.createElement('td'); td.innerText = item['repeats']; tr.appendChild(td);
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let td = document.createElement('td'); td.innerHTML = '<a href="https://www.pbs.gov.au/medicine/item/' + item['code'] + '" target="_blank">' + item['code'] + '</a>'; tr.appendChild(td);
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td = document.createElement('td'); td.innerText = item['mpp_preferred_term']; tr.appendChild(td);
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td = document.createElement('td'); td.innerText = item['maximum_prescribable_units']; tr.appendChild(td);
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td = document.createElement('td'); td.innerText = item['number_repeats']; tr.appendChild(td);
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if (item['restriction_flag'] === 'U') {
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if (item['benefit_type'] === 'unrestricted') {
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td = document.createElement('td'); tr.appendChild(td);
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} else if (item['restriction_flag'] === 'R') {
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td = document.createElement('td'); td.innerHTML = '<a href="https://www.pbs.gov.au/medicine/item/' + item['item_code'] + '" target="_blank">Restricted</a>'; tr.appendChild(td);
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} else if (item['benefit_type'] === 'restricted') {
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td = document.createElement('td'); td.innerHTML = '<a href="https://www.pbs.gov.au/medicine/item/' + item['code'] + '" target="_blank">Restricted</a>'; tr.appendChild(td);
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tr.classList.add('table-warning');
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} else if (item['restriction_flag'] === 'A') {
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if (item['streamlined_authorities'] > 0) {
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td = document.createElement('td'); td.innerHTML = '<a href="https://www.pbs.gov.au/medicine/item/' + item['item_code'] + '" target="_blank">Streamlined</a>'; tr.appendChild(td);
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tr.classList.add('table-warning');
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} else {
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td = document.createElement('td'); td.innerHTML = '<a href="https://www.pbs.gov.au/medicine/item/' + item['item_code'] + '" target="_blank">Authority</a>'; tr.appendChild(td);
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tr.classList.add('table-danger');
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}
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} else if (item['benefit_type'] === 'streamlined') {
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td = document.createElement('td'); td.innerHTML = '<a href="https://www.pbs.gov.au/medicine/item/' + item['code'] + '" target="_blank">Streamlined</a>'; tr.appendChild(td);
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tr.classList.add('table-warning');
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} else if (item['benefit_type'] === 'authority') {
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td = document.createElement('td'); td.innerHTML = '<a href="https://www.pbs.gov.au/medicine/item/' + item['code'] + '" target="_blank">Authority</a>'; tr.appendChild(td);
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tr.classList.add('table-danger');
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} else {
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td = document.createElement('td'); td.innerText = item['restriction_flag']; tr.appendChild(td);
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alert('Unknown benefit type: ' + item['benefit_type']);
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throw 'Unknown benefit type: ' + item['benefit_type'];
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}
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tbody.appendChild(tr);
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@ -126,17 +125,17 @@
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function comparePBSItems(item1, item2) {
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// Sort tablets/capsules before other forms
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if ((item1['tpuu_or_mpp_pt'].indexOf(' tablet, ') >= 0 || item1['tpuu_or_mpp_pt'].indexOf(' capsule, ') >= 0) && !(item2['tpuu_or_mpp_pt'].indexOf(' tablet, ') >= 0 || item2['tpuu_or_mpp_pt'].indexOf(' capsule, ') >= 0)) {
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if ((item1['mpp_preferred_term'].indexOf(' tablet, ') >= 0 || item1['mpp_preferred_term'].indexOf(' capsule, ') >= 0) && !(item2['mpp_preferred_term'].indexOf(' tablet, ') >= 0 || item2['mpp_preferred_term'].indexOf(' capsule, ') >= 0)) {
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return -1;
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}
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if ((item2['tpuu_or_mpp_pt'].indexOf(' tablet, ') >= 0 || item2['tpuu_or_mpp_pt'].indexOf(' capsule, ') >= 0) && !(item1['tpuu_or_mpp_pt'].indexOf(' tablet, ') >= 0 || item1['tpuu_or_mpp_pt'].indexOf(' capsule, ') >= 0)) {
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if ((item2['mpp_preferred_term'].indexOf(' tablet, ') >= 0 || item2['mpp_preferred_term'].indexOf(' capsule, ') >= 0) && !(item1['mpp_preferred_term'].indexOf(' tablet, ') >= 0 || item1['mpp_preferred_term'].indexOf(' capsule, ') >= 0)) {
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return 1;
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}
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// Compare tpuu_or_mpp_pt word-by-word accounting for numbers
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// Compare mpp_preferred_term word-by-word accounting for numbers
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const bits1 = item1['tpuu_or_mpp_pt'].split(' ');
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const bits2 = item2['tpuu_or_mpp_pt'].split(' ');
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const bits1 = item1['mpp_preferred_term'].split(' ');
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const bits2 = item2['mpp_preferred_term'].split(' ');
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for (let i = 0; i < bits1.length && i < bits2.length; i++) {
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if (regexIsNumber.test(bits1[i]) && regexIsNumber.test(bits2[i])) {
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@ -163,8 +162,8 @@
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// Sort unrestricted, then restricted/streamlined, then authority required
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const type1 = item1['restriction_flag'] === 'U' ? 0 : item1['restriction_flag'] === 'R' ? 1 : item1['restriction_flag'] === 'S' ? 1 : item1['streamlined_authorities'] > 0 ? 2 : 3;
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const type2 = item2['restriction_flag'] === 'U' ? 0 : item2['restriction_flag'] === 'R' ? 1 : item2['restriction_flag'] === 'S' ? 1 : item2['streamlined_authorities'] > 0 ? 2 : 3;
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const type1 = item1['benefit_type'] === 'unrestricted' ? 0 : item1['benefit_type'] === 'restricted' ? 1 : item1['benefit_type'] === 'streamlined' ? 1 : 2;
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const type2 = item2['benefit_type'] === 'unrestricted' ? 0 : item2['benefit_type'] === 'restricted' ? 1 : item2['benefit_type'] === 'streamlined' ? 1 : 2;
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return type1 - type2;
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}
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@ -1,64 +0,0 @@
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# Copyright © 2023 Lee Yingtong Li (RunasSudo)
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#
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# This program is free software: you can redistribute it and/or modify
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# it under the terms of the GNU Affero General Public License as published by
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# the Free Software Foundation, either version 3 of the License, or
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# (at your option) any later version.
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#
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# This program is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU Affero General Public License for more details.
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#
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# You should have received a copy of the GNU Affero General Public License
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# along with this program. If not, see <https://www.gnu.org/licenses/>.
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import pandas as pd
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import sqlite3
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import zipfile
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con = sqlite3.connect('database.db')
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cur = con.cursor()
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# Init schema
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cur.execute('DROP TABLE IF EXISTS pbs_drug')
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cur.execute('CREATE TABLE pbs_drug (id INTEGER PRIMARY KEY AUTOINCREMENT, item_code CHARACTER(6), mp_pt TEXT, tpuu_or_mpp_pt TEXT, restriction_flag CHARACTER(1), mq INTEGER, repeats INTEGER)')
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cur.execute('DROP TABLE IF EXISTS pbs_prescriber_type')
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cur.execute('CREATE TABLE pbs_prescriber_type (id INTEGER PRIMARY KEY AUTOINCREMENT, item_code CHARACTER(6), prescriber_type CHARACTER(1))')
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cur.execute('DROP TABLE IF EXISTS pbs_streamlined')
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cur.execute('CREATE TABLE pbs_streamlined (id INTEGER PRIMARY KEY AUTOINCREMENT, item_code CHARACTER(6), treatment_of_code INTEGER)')
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# Read drug list, prescriber type
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with zipfile.ZipFile('data/2023-01-01-v3extracts.zip', 'r') as zipf:
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# drug_xxx.txt
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with zipf.open('drug_20230101.txt', 'r') as f:
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df_drug = pd.read_csv(f, sep='!')
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for _, drug in df_drug.iterrows():
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# Skip already added
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cur.execute('SELECT COUNT(*) FROM pbs_drug WHERE item_code=?', (drug['item-code'],))
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if cur.fetchone()[0] > 0:
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continue
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cur.execute('INSERT INTO pbs_drug (item_code, mp_pt, tpuu_or_mpp_pt, restriction_flag, mq, repeats) VALUES (?, ?, ?, ?, ?, ?)', (drug['item-code'], drug['mp-pt'], drug['tpuu-or-mpp-pt'], drug['restriction-flag'], drug['mq'], drug['repeats']))
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# Prescriber_type_xxx.txt
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with zipf.open('Prescriber_type_20230101.txt', 'r') as f:
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df_prescriber_type = pd.read_csv(f, sep='\t', header=0, names=['mp-pt', 'item-code', 'prescriber-type'])
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for _, prescriber_type in df_prescriber_type.iterrows():
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cur.execute('INSERT INTO pbs_prescriber_type (item_code, prescriber_type) VALUES (?, ?)', (prescriber_type['item-code'], prescriber_type['prescriber-type']))
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# streamlined_xxx.txt (streamlined authorities)
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with zipf.open('streamlined_20230101.txt', 'r') as f:
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df_streamlined = pd.read_csv(f, sep='\t')
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for _, streamlined in df_streamlined.iterrows():
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cur.execute('INSERT INTO pbs_streamlined (item_code, treatment_of_code) VALUES (?, ?)', (streamlined['item-code'], streamlined['treatment-of-code']))
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con.commit()
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167
import_pbs_xml.py
Normal file
167
import_pbs_xml.py
Normal file
@ -0,0 +1,167 @@
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# Copyright © 2023 Lee Yingtong Li (RunasSudo)
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#
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# This program is free software: you can redistribute it and/or modify
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# it under the terms of the GNU Affero General Public License as published by
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# the Free Software Foundation, either version 3 of the License, or
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# (at your option) any later version.
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#
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# This program is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU Affero General Public License for more details.
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#
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# You should have received a copy of the GNU Affero General Public License
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# along with this program. If not, see <https://www.gnu.org/licenses/>.
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import sqlite3
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import zipfile
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from xml.etree import ElementTree as ET
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# Open database
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con = sqlite3.connect('database.db')
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cur = con.cursor()
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# Init schema
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cur.execute('DROP TABLE IF EXISTS pbs_item')
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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)')
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cur.execute('DROP TABLE IF EXISTS pbs_item_restriction')
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cur.execute('CREATE TABLE pbs_item_restriction (item_code TEXT, restriction_code INTEGER)')
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cur.execute('DROP TABLE IF EXISTS pbs_restriction')
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cur.execute('CREATE TABLE pbs_restriction (code INTEGER PRIMARY KEY, treatment_of INTEGER, indication TEXT, criteria_operator TEXT)')
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cur.execute('DROP TABLE IF EXISTS pbs_restriction_criteria')
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cur.execute('CREATE TABLE pbs_restriction_criteria (restriction_code INTEGER, criteria_code INTEGER)')
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cur.execute('DROP TABLE IF EXISTS pbs_criteria')
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cur.execute('CREATE TABLE pbs_criteria (code INTEGER PRIMARY KEY, type TEXT, parameters_operator TEXT)')
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cur.execute('DROP TABLE IF EXISTS pbs_criteria_parameter')
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cur.execute('CREATE TABLE pbs_criteria_parameter (id INTEGER PRIMARY KEY AUTOINCREMENT, criteria_code INTEGER, text TEXT)')
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# Parse XML
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with zipfile.ZipFile('data/2023-01-01-xml-V3.zip', 'r') as zipf:
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with zipf.open('sch-2023-01-01-r1.xml', 'r') as f:
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tree = ET.parse(f)
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print('Parsed XML')
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root = tree.getroot()
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ns = {'pbs': 'http://schema.pbs.gov.au/', 'xlink': 'http://www.w3.org/1999/xlink', 'xml': 'http://www.w3.org/XML/1998/namespace', 'rdf': 'http://www.w3.org/1999/02/22-rdf-syntax-ns#', 'dbk': 'http://docbook.org/ns/docbook'}
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# Get General Schedule
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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')
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restrictions_to_parse = set()
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criteria_to_parse = set()
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# Get schedule items (prescribing-rule) in schedule
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for item in program.findall('pbs:prescribing-rule', ns):
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code = item.find('pbs:code', ns).text
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# Only get benefits available to medical practitioners
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benefits = [b for b in item.find('pbs:benefit-types-list', ns).findall('pbs:benefit-type', ns) if b.find('pbs:member-of-list', ns).find('pbs:member-of[@rdf:resource="http://pbs.gov.au/prescriber/medical"]', ns)]
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if not benefits:
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continue
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assert len(benefits) == 1
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benefit = benefits[0]
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mpp_id = item.find('pbs:ready-prepared', ns).find('pbs:mpp-reference', ns).get('{http://www.w3.org/1999/xlink}href').lstrip('#')
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mpp = root.find('pbs:drugs-list', ns).find('pbs:mpp[@xml:id="' + mpp_id + '"]', ns)
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mpp_preferred_term = mpp.find('pbs:preferred-term', ns).text
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mp_id = mpp.find('pbs:drug-references-list', ns).find('pbs:mp-reference', ns).get('{http://www.w3.org/1999/xlink}href').lstrip('#')
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mp = root.find('pbs:drugs-list', ns).find('pbs:mp[@xml:id="' + mp_id + '"]', ns)
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mp_preferred_term = mp.find('pbs:preferred-term[@rdf:resource="http://pbs.gov.au/clinical"]', ns).text
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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
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max_repeats = item.find('pbs:ready-prepared', ns).find('pbs:number-repeats', ns).find('pbs:value', ns).text
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benefit_type = {
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'http://pbs.gov.au/benefit-type/unrestricted': 'unrestricted',
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'http://pbs.gov.au/benefit-type/restricted': 'restricted',
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'http://pbs.gov.au/benefit-type/streamlined': 'streamlined',
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'http://pbs.gov.au/benefit-type/authority-required': 'authority',
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}[benefit.get('{http://www.w3.org/1999/02/22-rdf-syntax-ns#}resource')]
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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))
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# Get restrictions
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if restrictions := benefit.find('pbs:restriction-references-list', ns):
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for restriction_reference in restrictions.findall('pbs:restriction-reference', ns):
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restriction_id = restriction_reference.get('{http://www.w3.org/1999/xlink}href').lstrip('#')
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restriction_code = restriction_reference.find('pbs:code', ns).text
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cur.execute('INSERT INTO pbs_item_restriction (item_code, restriction_code) VALUES (?, ?)', (code, restriction_code))
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# Queue this restriction for parsing
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restrictions_to_parse.add(restriction_id)
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# Parse restrictions
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for restriction_id in sorted(list(restrictions_to_parse)):
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restriction = root.find('pbs:prescribing-texts-list', ns).find('pbs:restriction[@xml:id="' + restriction_id + '"]', ns)
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code = restriction.find('pbs:code[@rdf:resource="http://pbs.gov.au/code/restriction"]', ns).text
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treatment_of = restriction.find('pbs:code[@rdf:resource="http://pbs.gov.au/code/treatment-of"]', ns).text
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# Build the name of the indication (episodicity, severity, condition)
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indication_id = restriction.find('pbs:indication-reference', ns).get('{http://www.w3.org/1999/xlink}href').lstrip('#')
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indication = root.find('pbs:prescribing-texts-list', ns).find('pbs:indication[@xml:id="' + indication_id + '"]', ns)
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indication_strings = []
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if episodicity_reference := indication.find('pbs:episodicity-reference', ns):
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episodicity_id = episodicity_reference.get('{http://www.w3.org/1999/xlink}href').lstrip('#')
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episodicity = root.find('pbs:prescribing-texts-list', ns).find('pbs:episodicity[@xml:id="' + episodicity_id + '"]', ns)
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episodicity_term = episodicity.find('pbs:preferred-term', ns).text.strip()
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indication_strings.append(episodicity_term)
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if severity_reference := indication.find('pbs:severity-reference', ns):
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severity_id = severity_reference.get('{http://www.w3.org/1999/xlink}href').lstrip('#')
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severity = root.find('pbs:prescribing-texts-list', ns).find('pbs:severity[@xml:id="' + severity_id + '"]', ns)
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severity_term = severity.find('pbs:preferred-term', ns).text.strip()
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indication_strings.append(severity_term)
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condition_id = indication.find('pbs:condition-reference', ns).get('{http://www.w3.org/1999/xlink}href').lstrip('#')
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condition = root.find('pbs:prescribing-texts-list', ns).find('pbs:condition[@xml:id="' + condition_id + '"]', ns)
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condition_term = condition.find('pbs:preferred-term', ns).text.strip()
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indication_strings.append(condition_term)
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# Get operator and criteria
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operators = restriction.findall('pbs:any', ns) + restriction.findall('pbs:all', ns) + restriction.findall('pbs:one-of', ns)
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if operators:
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operator = operators[0].tag[operators[0].tag.index('}')+1:]
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for criteria_reference in operators[0].findall('pbs:criteria-reference', ns):
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criteria_id = criteria_reference.get('{http://www.w3.org/1999/xlink}href').lstrip('#')
|
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criteria_code = criteria_reference.find('pbs:code', ns).text
|
||||
cur.execute('INSERT INTO pbs_restriction_criteria (restriction_code, criteria_code) VALUES (?, ?)', (code, criteria_code))
|
||||
|
||||
# Queue this criteria for parsing
|
||||
criteria_to_parse.add(criteria_id)
|
||||
else:
|
||||
operator = None
|
||||
|
||||
cur.execute('INSERT INTO pbs_restriction (code, treatment_of, indication, criteria_operator) VALUES (?, ?, ?, ?)', (code, treatment_of, ' '.join(indication_strings), operator))
|
||||
|
||||
# Parse criteria
|
||||
for criteria_id in sorted(list(criteria_to_parse)):
|
||||
criteria = root.find('pbs:prescribing-texts-list', ns).find('*[@xml:id="' + criteria_id + '"]', ns)
|
||||
criteria_type = criteria.tag[criteria.tag.index('}')+1:]
|
||||
code = criteria.find('pbs:code', ns).text
|
||||
|
||||
# Get operator and parameters
|
||||
operators = criteria.findall('pbs:any', ns) + criteria.findall('pbs:all', ns) + criteria.findall('pbs:one-of', ns)
|
||||
if operators:
|
||||
operator = operators[0].tag[operators[0].tag.index('}')+1:]
|
||||
|
||||
for parameter_reference in operators[0].findall('pbs:parameter-reference', ns):
|
||||
parameter_id = parameter_reference.get('{http://www.w3.org/1999/xlink}href').lstrip('#')
|
||||
parameter = root.find('pbs:prescribing-texts-list', ns).find('*[@xml:id="' + parameter_id + '"]', ns)
|
||||
|
||||
note_text = '\n'.join(p.text for n in parameter.findall('dbk:note', ns) for p in n.findall('dbk:para', ns))
|
||||
cur.execute('INSERT INTO pbs_criteria_parameter (criteria_code, text) VALUES (?, ?)', (code, note_text))
|
||||
|
||||
cur.execute('INSERT INTO pbs_criteria (code, type, parameters_operator) VALUES (?, ?, ?)', (code, criteria_type, operator))
|
||||
|
||||
con.commit()
|
||||
Loading…
Reference in New Issue
Block a user