RunasSudo/MedicineSearch
1
Fork 0
Code Issues 2 Pull Requests Releases Activity

Allow searching by trade name

Browse Source
This commit is contained in:
RunasSudo 2023-01-24 19:56:54 +11:00
parent 8967b3e5b9
commit 96c9e962e1
Signed by: RunasSudo
GPG Key ID: 7234E476BF21C61A
5 changed files with 114 additions and 9 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
export_db.sh
View File

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

84
find_pbs_brand_names.py Normal file
View File

@ -0,0 +1,84 @@
# Copyright © 2023 Lee Yingtong Li (RunasSudo)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
import re
import sqlite3
LOOKS_LIKE_DOSE = re.compile(r'([0-9/.,+%]*( ?(mg|mL|U|IU))?)+')
# Open database
con = sqlite3.connect('database.db')
con.row_factory = sqlite3.Row
cur = con.cursor()
# Init schema
cur.execute('DROP TABLE IF EXISTS pbs_mp_brand_name')
cur.execute('CREATE TABLE pbs_mp_brand_name (id INTEGER PRIMARY KEY AUTOINCREMENT, mp_code STRING, brand_name STRING)')
cur.execute('SELECT * FROM pbs_tpp LEFT JOIN (SELECT code, mp_code FROM pbs_mpp) AS pbs_mpp ON pbs_tpp.mpp_code = pbs_mpp.code LEFT JOIN (SELECT code, preferred_term as mp_preferred_term FROM pbs_mp) AS pbs_mp ON pbs_mpp.mp_code = pbs_mp.code')
brand_names = {}
for tpp in cur.fetchall():
words = tpp['brand_name'].split()
words_lower = tpp['brand_name'].lower().split()
# If any word of the generic name is in the brand name, skip it because it is uninteresting
if any(w.lower() in tpp['brand_name'].lower() for w in tpp['mp_preferred_term'].split() if w != '+'):
continue
# Ignore anything that looks like a company name
if 'pty' in words_lower or 'ltd' in words_lower or 'australia' in words_lower:
continue
# Strip all trailing words that look like a dose
for i in reversed(range(len(words))):
if LOOKS_LIKE_DOSE.fullmatch(words[i]):
del words[i]
else:
break
# OK!
brand_name = ' '.join(words)
if tpp['mp_code'] not in brand_names:
brand_names[tpp['mp_code']] = set()
brand_names[tpp['mp_code']].add(brand_name)
# Reduce names with unambiguous prefixes
for mp_code in sorted(brand_names.keys()):
for brand_name in list(brand_names[mp_code]):
# Can we reduce the length of the name?
words = brand_name.split()
for i in range(1, len(words)):
short_name = ' '.join(words[0:i])
if any(b.startswith(short_name) for m in brand_names.keys() if m != mp_code for b in brand_names[m]):
# Conflict
continue
# Can shorten
if brand_name in brand_names[mp_code]:
brand_names[mp_code].remove(brand_name)
brand_names[mp_code].add(short_name)
break
# Add to database
for mp_code in sorted(brand_names.keys()):
for brand_name in sorted(list(brand_names[mp_code])):
cur.execute('INSERT INTO pbs_mp_brand_name (mp_code, brand_name) VALUES (?, ?)', (mp_code, brand_name))
con.commit()

12
html/autocomplete.js
View File

@ -75,11 +75,11 @@ class Autocomplete {
.indexOf(removeDiacritics(lookup).toLowerCase());
const className = Array.isArray(this.options.highlightClass) ? this.options.highlightClass.join(' ')
: (typeof this.options.highlightClass == 'string' ? this.options.highlightClass : '');
label = item.label.substring(0, idx)
+ `<span class="${className}">${item.label.substring(idx, idx + lookup.length)}</span>`
+ item.label.substring(idx + lookup.length, item.label.length);
label = item.preview.substring(0, idx)
+ `<span class="${className}">${item.preview.substring(idx, idx + lookup.length)}</span>`
+ item.preview.substring(idx + lookup.length, item.preview.length);
} else {
label = item.label;
label = item.preview;
}
if (this.options.showValue) {
@ -128,7 +128,8 @@ class Autocomplete {
const entry = this.options.data[key];
const item = {
label: this.options.label ? entry[this.options.label] : key,
value: this.options.value ? entry[this.options.value] : entry
preview: entry.preview,
value: this.options.value ? entry[this.options.value] : entry,
};
if (removeDiacritics(item.label).toLowerCase().indexOf(removeDiacritics(lookup).toLowerCase()) == 0) {
@ -144,6 +145,7 @@ class Autocomplete {
const entry = this.options.data[key];
const item = {
label: this.options.label ? entry[this.options.label] : key,
preview: entry.preview,
value: this.options.value ? entry[this.options.value] : entry
};

13
html/index.html
View File

@ -76,8 +76,12 @@
db = new SQL.Database(new Uint8Array(buf));
// Initialise search bar
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 mp_preferred_terms = execAsScalars(db.prepare('SELECT preferred_term FROM pbs_mp ORDER BY LOWER(preferred_term)'));
let data = mp_preferred_terms.map(mp_preferred_term => ({'label': mp_preferred_term, 'preview': mp_preferred_term, 'value': mp_preferred_term}));
const tpp_brand_names = execAsObjects(db.prepare('SELECT * FROM pbs_mp_brand_name LEFT JOIN pbs_mp ON pbs_mp_brand_name.mp_code = pbs_mp.code ORDER BY LOWER(brand_name)'));
data = data.concat(tpp_brand_names.map(tpp_brand_name => ({'label': tpp_brand_name['brand_name'], 'preview': tpp_brand_name['brand_name'] + ' <span class="text-muted">(' + tpp_brand_name['preferred_term'] + ')</span>', 'value': tpp_brand_name['preferred_term']})));
const autocomplete = new Autocomplete(document.getElementById('search-input'), {
data: data,
maximumItems: 20,
@ -87,9 +91,12 @@
}
function onClickSearchItem(item) {
// Override label if clicked on a trade name
document.getElementById('search-input').value = item.value;
// Find matching PBS items
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()]);
stmt.bind([item.value.toLowerCase()]);
const items = execAsObjects(stmt);
items.sort(comparePBSItems);

12
import_pbs_xml.py
View File

@ -28,6 +28,9 @@ cur.execute('CREATE TABLE pbs_item (code TEXT PRIMARY KEY, mpp_code TEXT, maximu
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_tpp')
cur.execute('CREATE TABLE pbs_tpp (code TEXT PRIMARY KEY, mpp_code TEXT, brand_name TEXT)')
cur.execute('DROP TABLE IF EXISTS pbs_mp')
cur.execute('CREATE TABLE pbs_mp (code TEXT PRIMARY KEY, preferred_term TEXT)')
@ -60,6 +63,7 @@ ns = {'pbs': 'http://schema.pbs.gov.au/', 'xlink': 'http://www.w3.org/1999/xlink
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()
tpps_to_parse = set()
mps_to_parse = set()
restrictions_to_parse = set()
criteria_to_parse = set()
@ -135,6 +139,14 @@ for mp_id in sorted(list(mps_to_parse)):
cur.execute('INSERT INTO pbs_mp (code, preferred_term) VALUES (?, ?)', (mp_code, mp_preferred_term))
# Parse TPPs
for (tpp_id, mpp_code) in sorted(list(tpps_to_parse)):
tpp = root.find('pbs:drugs-list', ns).find('pbs:tpp[@xml:id="' + tpp_id + '"]', ns)
tpp_code = tpp.find('pbs:code', ns).text
tpp_brand_name = tpp.find('pbs:brand-name', ns).find('pbs:value', ns).text
cur.execute('INSERT INTO pbs_tpp (code, mpp_code, brand_name) VALUES (?, ?, ?)', (tpp_code, mpp_code, tpp_brand_name))
# Parse restrictions
for restriction_id in sorted(list(restrictions_to_parse)):
restriction = root.find('pbs:prescribing-texts-list', ns).find('pbs:restriction[@xml:id="' + restriction_id + '"]', ns)