diff options
Diffstat (limited to 'plip/exchange/webservices.py')
| -rw-r--r-- | plip/exchange/webservices.py | 40 |
1 files changed, 23 insertions, 17 deletions
diff --git a/plip/exchange/webservices.py b/plip/exchange/webservices.py index 0c8cd3e..61cb6f5 100644 --- a/plip/exchange/webservices.py +++ b/plip/exchange/webservices.py @@ -11,44 +11,50 @@ logger = logger.get_logger() def check_pdb_status(pdbid): """Returns the status and up-to-date entry in the PDB for a given PDB ID""" - url = 'http://www.rcsb.org/pdb/rest/idStatus?structureId=%s' % pdbid + url = "http://www.rcsb.org/pdb/rest/idStatus?structureId=%s" % pdbid xmlf = urlopen(url) xml = et.parse(xmlf) xmlf.close() status = None current_pdbid = pdbid - for df in xml.xpath('//record'): - status = df.attrib['status'] # Status of an entry can be either 'UNKWOWN', 'OBSOLETE', or 'CURRENT' - if status == 'OBSOLETE': - current_pdbid = df.attrib['replacedBy'] # Contains the up-to-date PDB ID for obsolete entries + for df in xml.xpath("//record"): + status = df.attrib[ + "status" + ] # Status of an entry can be either 'UNKWOWN', 'OBSOLETE', or 'CURRENT' + if status == "OBSOLETE": + current_pdbid = df.attrib[ + "replacedBy" + ] # Contains the up-to-date PDB ID for obsolete entries return [status, current_pdbid.lower()] def fetch_pdb(pdbid): """Get the newest entry from the RCSB server for the given PDB ID. Exits with '1' if PDB ID is invalid.""" pdbid = pdbid.lower() - logger.info(f'checking status of PDB-ID {pdbid}') + logger.info(f"checking status of PDB-ID {pdbid}") state, current_entry = check_pdb_status(pdbid) # Get state and current PDB ID - if state == 'OBSOLETE': - logger.info(f'entry is obsolete, getting {current_entry} instead') - elif state == 'CURRENT': - logger.info('entry is up-to-date') - elif state == 'UNKNOWN': - logger.error('invalid PDB-ID (entry does not exist on PDB server)') + if state == "OBSOLETE": + logger.info(f"entry is obsolete, getting {current_entry} instead") + elif state == "CURRENT": + logger.info("entry is up-to-date") + elif state == "UNKNOWN": + logger.error("invalid PDB-ID (entry does not exist on PDB server)") sys.exit(1) - logger.info('downloading file from PDB') + logger.info("downloading file from PDB") # get URL for current entry # @todo needs update to react properly on response codes of RCSB servers - pdburl = f'http://www.rcsb.org/pdb/files/{current_entry}.pdb' + pdburl = f"http://www.rcsb.org/pdb/files/{current_entry}.pdb" try: pdbfile = urlopen(pdburl).read().decode() # If no PDB file is available, a text is now shown with "We're sorry, but ..." # Could previously be distinguished by an HTTP error - if 'sorry' in pdbfile: - logger.error('no file in PDB format available from wwPDB for the given PDB ID.') + if "sorry" in pdbfile: + logger.error( + "no file in PDB format available from wwPDB for the given PDB ID." + ) sys.exit(1) except HTTPError: - logger.error('no file in PDB format available from wwPDB for the given PDB ID') + logger.error("no file in PDB format available from wwPDB for the given PDB ID") sys.exit(1) return [pdbfile, current_entry] |