Nilesh Patra pushed to branch master at Debian Med / plip
Commits: fa203c5e by Nilesh Patra at 2020-11-11T19:26:02+05:30 routine-update: New upstream version - - - - - a768dc00 by Nilesh Patra at 2020-11-11T19:26:03+05:30 New upstream version 2.1.6+dfsg - - - - - 1e897113 by Nilesh Patra at 2020-11-11T19:26:04+05:30 Update upstream source from tag 'upstream/2.1.6+dfsg' Update to upstream version '2.1.6+dfsg' with Debian dir 98dd581b8bc780c60c43e35db634ee2dc30ba43d - - - - - 100be139 by Nilesh Patra at 2020-11-11T19:26:15+05:30 routine-update: Ready to upload to unstable - - - - - 5 changed files: - CHANGES.txt - debian/changelog - 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 ===================================== debian/changelog ===================================== @@ -1,3 +1,10 @@ +plip (2.1.6+dfsg-1) unstable; urgency=medium + + * Team upload. + * New upstream version + + -- Nilesh Patra <[email protected]> Wed, 11 Nov 2020 19:26:15 +0530 + plip (2.1.5+dfsg-1) unstable; urgency=medium * Team upload. ===================================== 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/-/compare/43291b9a3cac609068606ad2906c96baf9825fb1...100be1392e5ba13088463cbaa491d23d40117d2b -- View it on GitLab: https://salsa.debian.org/med-team/plip/-/compare/43291b9a3cac609068606ad2906c96baf9825fb1...100be1392e5ba13088463cbaa491d23d40117d2b You're receiving this email because of your account on salsa.debian.org.
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