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

Fix idiosyncratic entries for metoprolol

Browse Source
This commit is contained in:
RunasSudo 2023-02-04 16:03:12 +11:00
parent eddbdfcccf
commit 0541f5f063
Signed by: RunasSudo
GPG Key ID: 7234E476BF21C61A
1 changed files with 21 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

22
import_pbs_xml.py
View File

@ -140,10 +140,26 @@ for mpp_id in sorted(list(mpps_to_parse)):
mp = root.find('pbs:drugs-list', ns).find('pbs:mp[@xml:id="' + mp_id + '"]', ns) 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 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
# Manual fixups for metoprolol
if 'METOPROLOL' in mpp_preferred_term:
# Incorrect capitalisation
mpp_preferred_term = mpp_preferred_term.replace('METOPROLOL SUCCINATE Tablet', 'metoprolol succinate')
mpp_preferred_term = mpp_preferred_term.replace('METOPROLOL TARTRATE Tablet', 'metoprolol tartrate')
# Idiosyncratic word order
mpp_preferred_term = mpp_preferred_term.replace('(controlled release)', 'modified release tablet')
mpp_preferred_term = mpp_preferred_term.replace('mg,', 'mg tablet,')
# Classify as "metoprolol tartrate"
if mp_code == '1187PBSC':
mp_id = None
mp_code = '432PBSC'
cur.execute('INSERT INTO pbs_mpp (code, mp_code, preferred_term) VALUES (?, ?, ?)', (mpp_code, mp_code, mpp_preferred_term)) cur.execute('INSERT INTO pbs_mpp (code, mp_code, preferred_term) VALUES (?, ?, ?)', (mpp_code, mp_code, mpp_preferred_term))
# Queue the MP for parsing # Queue the MP for parsing
mps_to_parse.add(mp_id) if mp_id:
mps_to_parse.add(mp_id)
# Get TPPs # Get TPPs
for tpp_reference in mpp.find('pbs:drug-references-list', ns).findall('pbs:tpp-reference', ns): for tpp_reference in mpp.find('pbs:drug-references-list', ns).findall('pbs:tpp-reference', ns):
@ -158,6 +174,10 @@ for mp_id in sorted(list(mps_to_parse)):
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_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 mp_preferred_term = mp.find('pbs:preferred-term[@rdf:resource="http://pbs.gov.au/clinical"]', ns).text
if mp_code == '432PBSC':
# Specified as all uppercase in PBS XML for some reason
mp_preferred_term = 'metoprolol'
cur.execute('INSERT INTO pbs_mp (code, preferred_term) VALUES (?, ?)', (mp_code, mp_preferred_term)) cur.execute('INSERT INTO pbs_mp (code, preferred_term) VALUES (?, ?)', (mp_code, mp_preferred_term))
# Parse TPPs # Parse TPPs