initial commit

1 files changed, 54 insertions, 0 deletions

diff --git a/plip/exchange/webservices.py b/plip/exchange/webservices.py
new file mode 100644
index 0000000..0c8cd3e
--- /dev/null
+++ b/plip/exchange/webservices.py
@@ -0,0 +1,54 @@
+import sys
+from urllib.error import HTTPError
+from urllib.request import urlopen
+
+import lxml.etree as et
+
+from plip.basic import logger
+
+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
+    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
+    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}')
+    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+        logger.info(f'entry is obsolete, getting {current_entry} instead')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)')
+        sys.exit(1)
+    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'
+    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.')
+            sys.exit(1)
+    except HTTPError:
+        logger.error('no file in PDB format available from wwPDB for the given PDB ID')
+        sys.exit(1)
+    return [pdbfile, current_entry]