Nilesh Patra pushed to branch upstream at Debian Med / plip
Commits: a768dc00 by Nilesh Patra at 2020-11-11T19:26:03+05:30 New upstream version 2.1.6+dfsg - - - - - 4 changed files: - CHANGES.txt - plip/basic/config.py - plip/exchange/webservices.py - plip/test/test_command_line.py Changes: ===================================== CHANGES.txt ===================================== @@ -1,5 +1,8 @@ Changelog --------- +# 2.1.6 +* fetch URL for PDB files updated to avoid issues with RCSB API changes + # 2.1.5 * option added to handle specific model in NMR structures * fixes a bug in alt-location handling ===================================== plip/basic/config.py ===================================== @@ -1,4 +1,4 @@ -__version__ = '2.1.5' +__version__ = '2.1.6' __maintainer__ = 'PharmAI GmbH (2020) - www.pharm.ai - [email protected]' import logging ===================================== plip/exchange/webservices.py ===================================== @@ -27,7 +27,7 @@ def check_pdb_status(pdbid): 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}') # @todo re-implement state check with ew RCSB API, see https://www.rcsb.org/news?year=2020&article=5eb18ccfd62245129947212a&feature=true # state, current_entry = check_pdb_status(pdbid) # Get state and current PDB ID # @@ -41,7 +41,7 @@ def fetch_pdb(pdbid): 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/{pdbid}.pdb' + pdburl = f'https://files.rcsb.org/download/{pdbid}.pdb' try: pdbfile = urlopen(pdburl).read().decode() # If no PDB file is available, a text is now shown with "We're sorry, but ..." ===================================== plip/test/test_command_line.py ===================================== @@ -40,6 +40,11 @@ class CommandLineTest(unittest.TestCase): exitcode = subprocess.call(f'{sys.executable} ../plipcmd.py -i 4v59 -o {self.tmp_dir.name}', shell=True) self.assertEqual(exitcode, 1) + def test_pdb_format_available(self): + """A valid PDB ID is provided, but there is no entry in PDB format from wwPDB""" + exitcode = subprocess.call(f'{sys.executable} ../plipcmd.py -i 1acj -o {self.tmp_dir.name}', shell=True) + self.assertEqual(exitcode, 0) + def test_valid_pdb(self): """A PDB ID with no valid PDB record is provided.""" exitcode = subprocess.call(f'{sys.executable} ../plipcmd.py -x -f ./pdb/1eve.pdb -o {self.tmp_dir.name}', View it on GitLab: https://salsa.debian.org/med-team/plip/-/commit/a768dc00c77828ada9d16c06147786c880369d93 -- View it on GitLab: https://salsa.debian.org/med-team/plip/-/commit/a768dc00c77828ada9d16c06147786c880369d93 You're receiving this email because of your account on salsa.debian.org.
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